NM_177438.3:c.1419T>C

Variant names:

• chr14-95117712-A-G
• rs879221429
• NM_177438.3:c.1419T>C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 2P and 16B. PM2 BP4_Strong BP6_Very_Strong BS2

The NM_177438.3(DICER1):​c.1419T>C​(p.Tyr473Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,620 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000034 (0 hom.)
• Consequence: DICER1 NM_177438.3 synonymous
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 1.51
• Publications: 1 publications found

Genes affected

DICER1 (HGNC:17098): (dicer 1, ribonuclease III) This gene encodes a protein possessing an RNA helicase motif containing a DEXH box in its amino terminus and an RNA motif in the carboxy terminus. The encoded protein functions as a ribonuclease and is required by the RNA interference and small temporal RNA (stRNA) pathways to produce the active small RNA component that represses gene expression. This protein also acts as a strong antiviral agent with activity against RNA viruses, including the Zika and SARS-CoV-2 viruses. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2021]

DICER1 Gene-Disease associations (from GenCC):

• DICER1-related tumor predisposition

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• pleuropulmonary blastoma

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• DICER1 syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• global developmental delay - lung cysts - overgrowth - Wilms tumor syndrome

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BP6: Variant 14-95117712-A-G is Benign according to our data. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-95117712-A-G is described in CliVar as Likely_benign. Clinvar id is 543701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS2: High AC in GnomAdExome4 at 5 AD,Unknown gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DICER1	NM_177438.3	c.1419T>C	p.Tyr473Tyr	synonymous_variant	Exon 9 of 27	ENST00000343455.8	NP_803187.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DICER1	ENST00000343455.8	c.1419T>C	p.Tyr473Tyr	synonymous_variant	Exon 9 of 27	1	NM_177438.3	ENSP00000343745.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000342 AC: 5 AN: 1461620 Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5 AN XY: 727126

African (AFR) AF: 0.00 AC: 0 AN: 33464

American (AMR) AF: 0.00 AC: 0 AN: 44718

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26128

East Asian (EAS) AF: 0.00 AC: 0 AN: 39682

South Asian (SAS) AF: 0.0000580 AC: 5 AN: 86256

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53416

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1111812

Other (OTH) AF: 0.00 AC: 0 AN: 60376

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

DICER1-related tumor predisposition Benign:1

Jan 14, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary cancer-predisposing syndrome Benign:1

Nov 30, 2018

Ambry Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	6.3
DANN	Benign	0.49
PhyloP100		1.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs879221429; hg19: chr14-95584049;