Variant 3-14661341-A-AT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

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

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.674

Variant links:

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 links:

CCDC174 (HGNC:):

CCDC174 links:

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ACMG classification

Classification made for transcript

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 linkuse as main transcript	c.308-182dupT		intron_variant		ENST00000383794.7	NP_057558.3	Q6PII3

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
CCDC174	ENST00000383794.7 linkuse as main transcript	c.308-182dupT	intron_variant	1	NM_016474.5	ENSP00000373304.3	Q6PII3
CCDC174	ENST00000465759.1 linkuse as main transcript	n.372-182dupT	intron_variant	1
CCDC174	ENST00000303688.8 linkuse as main transcript	c.308-182dupT	intron_variant	5		ENSP00000302344.7	A0A0B4J1R8
CCDC174	ENST00000463438.5 linkuse as main transcript	n.381-182dupT	intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.438

AC:

66489

AN:

151720

Hom.:

16490

Cov.:

show subpopulations

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.:

AF XY:

0.437

AC XY:

32425

AN XY:

74198

show subpopulations

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

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 27, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over