chr3-14661341-A-AT

Position:

• chr3-14661341-A-AT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_016474.5(CCDC174):​c.308-182dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.44 (16484 hom., cov: 0)
• Consequence: CCDC174 NM_016474.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.674

Genes affected

CCDC174 (HGNC:28033): (coiled-coil domain containing 174) The protein encoded by this gene is found in the nucleus, where it interacts with eukaryotic translation initiation factor 4A, isoform 3. The encoded protein appears to be a part of the exon junction complex, which is involved in RNA processing, translation, and nonsense-mediated mRNA decay. A mutation in this gene has been associated with infantile hypotonia with psychomotor retardation. [provided by RefSeq, Mar 2016]

CCDC174 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 3-14661341-A-AT is Benign according to our data. Variant chr3-14661341-A-AT is described in ClinVar as [Benign]. Clinvar id is 1241316.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC174	NM_016474.5	c.308-182dupT		intron_variant		ENST00000383794.7	NP_057558.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC174	ENST00000383794.7	c.308-182dupT		intron_variant		1	NM_016474.5	ENSP00000373304.3
CCDC174	ENST00000465759.1	n.372-182dupT		intron_variant		1
CCDC174	ENST00000303688.8	c.308-182dupT		intron_variant		5		ENSP00000302344.7
CCDC174	ENST00000463438.5	n.381-182dupT		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66489 AN: 151720 Hom.: 16490 Cov.: 0

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.467

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.438 AC: 66499 AN: 151838 Hom.: 16484 Cov.: 0 AF XY: 0.437 AC XY: 32425 AN XY: 74198

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.465

Alfa AF: 0.285 Hom.: 582

Asia WGS AF: 0.532 AC: 1852 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 27, 2021

- -

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs3832217; hg19: chr3-14702848;