Variant 10-277343-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_014974.3(DIP2C):c.4653T>C(p.Tyr1551Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 1,613,930 control chromosomes in the GnomAD database, including 58,175 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.27 ( 5667 hom., cov: 32)

Exomes 𝑓: 0.27 ( 52508 hom. )

Consequence

DIP2C
NM_014974.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.124

Variant links:

Genes affected

DIP2C (HGNC:29150): (disco interacting protein 2 homolog C) This gene encodes a member of the disco-interacting protein homolog 2 family. The protein shares strong similarity with a Drosophila protein which interacts with the transcription factor disco and is expressed in the nervous system. [provided by RefSeq, Oct 2008]

DIP2C links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 10-277343-A-G is Benign according to our data. Variant chr10-277343-A-G is described in ClinVar as [Benign]. Clinvar id is 1598742.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.124 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DIP2C	NM_014974.3 linkuse as main transcript	c.4653T>C	p.Tyr1551Tyr	synonymous_variant	37/37	ENST00000280886.12	NP_055789.1	Q9Y2E4-1Q86XV3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DIP2C	ENST00000280886.12 linkuse as main transcript	c.4653T>C	p.Tyr1551Tyr	synonymous_variant	37/37	1	NM_014974.3	ENSP00000280886.6		Q9Y2E4-1
DIP2C	ENST00000634311.1 linkuse as main transcript	c.4851T>C	p.Tyr1617Tyr	synonymous_variant	39/39	5		ENSP00000489203.1		A0A0U1RQW6

Frequencies

GnomAD3 genomes

AF:

0.271

AC:

41183

AN:

152026

Hom.:

5657

Cov.:

show subpopulations

Gnomad AFR

AF:

0.296

Gnomad AMI

AF:

0.182

Gnomad AMR

AF:

0.234

Gnomad ASJ

AF:

0.221

Gnomad EAS

AF:

0.247

Gnomad SAS

AF:

0.342

Gnomad FIN

AF:

0.274

Gnomad MID

AF:

0.348

Gnomad NFE

AF:

0.263

Gnomad OTH

AF:

0.281

GnomAD3 exomes

AF:

0.265

AC:

66612

AN:

251334

Hom.:

9246

AF XY:

0.273

AC XY:

37127

AN XY:

135856

show subpopulations

Gnomad AFR exome

AF:

0.297

Gnomad AMR exome

AF:

0.180

Gnomad ASJ exome

AF:

0.230

Gnomad EAS exome

AF:

0.246

Gnomad SAS exome

AF:

0.355

Gnomad FIN exome

AF:

0.272

Gnomad NFE exome

AF:

0.266

Gnomad OTH exome

AF:

0.275

GnomAD4 exome

AF:

0.265

AC:

388057

AN:

1461786

Hom.:

52508

Cov.:

AF XY:

0.269

AC XY:

195913

AN XY:

727196

show subpopulations

Gnomad4 AFR exome

AF:

0.298

Gnomad4 AMR exome

AF:

0.188

Gnomad4 ASJ exome

AF:

0.230

Gnomad4 EAS exome

AF:

0.228

Gnomad4 SAS exome

AF:

0.354

Gnomad4 FIN exome

AF:

0.267

Gnomad4 NFE exome

AF:

0.262

Gnomad4 OTH exome

AF:

0.278

GnomAD4 genome

AF:

0.271

AC:

41199

AN:

152144

Hom.:

5667

Cov.:

AF XY:

0.272

AC XY:

20255

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.296

Gnomad4 AMR

AF:

0.233

Gnomad4 ASJ

AF:

0.221

Gnomad4 EAS

AF:

0.247

Gnomad4 SAS

AF:

0.343

Gnomad4 FIN

AF:

0.274

Gnomad4 NFE

AF:

0.263

Gnomad4 OTH

AF:

0.278

Alfa

AF:

0.266

Hom.:

12158

Bravo

AF:

0.264

Asia WGS

AF:

0.296

AC:

1027

AN:

3478

EpiCase

AF:

0.273

EpiControl

AF:

0.269

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

DIP2C-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 21, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

1.8

DANN

Benign

0.56

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