14-95107991-T-A

Variant names:

• chr14-95107991-T-A
• rs1060503641
• NM_177438.3:c.2539A>T

Variant summary

Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PM2 PM5

The NM_177438.3(DICER1):​c.2539A>T​(p.Thr847Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T847I) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: DICER1 NM_177438.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.92
• Publications: 0 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: Uncertain_significance. The variant received 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr14-95107991-TAATC-AATGCTTGAAGTTGATT is described in ClinVar as Likely_pathogenic. ClinVar VariationId is 933057.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_177438.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DICER1	NM_177438.3	MANE Select	c.2539A>T	p.Thr847Ser	missense	Exon 16 of 27	NP_803187.1
	DICER1	NM_001271282.3		c.2539A>T	p.Thr847Ser	missense	Exon 16 of 27	NP_001258211.1
	DICER1	NM_001291628.2		c.2539A>T	p.Thr847Ser	missense	Exon 16 of 27	NP_001278557.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DICER1	ENST00000343455.8	TSL:1 MANE Select	c.2539A>T	p.Thr847Ser	missense	Exon 16 of 27	ENSP00000343745.3
	DICER1	ENST00000393063.6	TSL:1	c.2539A>T	p.Thr847Ser	missense	Exon 18 of 29	ENSP00000376783.1
	DICER1	ENST00000527414.5	TSL:1	c.2539A>T	p.Thr847Ser	missense	Exon 16 of 27	ENSP00000435681.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Pathogenic	0.19	D
BayesDel_noAF	Uncertain	0.030
CADD	Benign	23
DANN	Uncertain	0.99
DEOGEN2	Benign	0.24	T
Eigen	Uncertain	0.21
Eigen_PC	Uncertain	0.31
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Benign	0.85	T
M_CAP	Benign	0.073	D
MetaRNN	Uncertain	0.50	T
MetaSVM	Benign	-0.65	T
MutationAssessor	Benign	1.9	M
PhyloP100		7.9
PrimateAI	Uncertain	0.71	T
PROVEAN	Benign	0.020	N
REVEL	Uncertain	0.55
Sift	Benign	0.44	T
Sift4G	Benign	0.74	T
Polyphen		0.96	D
Vest4		0.61
MutPred		0.40		Loss of catalytic residue at T847 (P = 0.0584)
MVP		0.88
MPC		0.85
ClinPred		0.78	D
GERP RS		4.7
Varity_R		0.46
gMVP		0.43
Mutation Taster		=57/43	polymorphism

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: rs1060503641; hg19: chr14-95574328;