Variant 15-65400920-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_020962.3(IGDCC4):c.727G>A(p.Asp243Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00976 in 1,614,186 control chromosomes in the GnomAD database, including 87 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0071 ( 3 hom., cov: 32)

Exomes 𝑓: 0.010 ( 84 hom. )

Consequence

IGDCC4
NM_020962.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.22

Variant links:

Genes affected

IGDCC4 (HGNC:13770): (immunoglobulin superfamily DCC subclass member 4) Predicted to be located in plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

IGDCC4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.00790751).

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGDCC4	NM_020962.3 linkuse as main transcript	c.727G>A	p.Asp243Asn	missense_variant	5/20	ENST00000352385.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IGDCC4	ENST00000352385.3 linkuse as main transcript	c.727G>A	p.Asp243Asn	missense_variant	5/20	1	NM_020962.3	P1	Q8TDY8-1

Frequencies

GnomAD3 genomes

AF:

0.00707

AC:

1076

AN:

152206

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00147

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.00615

Gnomad ASJ

AF:

0.00807

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00892

Gnomad FIN

AF:

0.0128

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0103

Gnomad OTH

AF:

0.00478

GnomAD3 exomes

AF:

0.00820

AC:

2061

AN:

251340

Hom.:

AF XY:

0.00855

AC XY:

1162

AN XY:

135860

show subpopulations

Gnomad AFR exome

AF:

0.00142

Gnomad AMR exome

AF:

0.00442

Gnomad ASJ exome

AF:

0.00834

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00964

Gnomad FIN exome

AF:

0.0142

Gnomad NFE exome

AF:

0.0102

Gnomad OTH exome

AF:

0.00669

GnomAD4 exome

AF:

0.0100

AC:

14676

AN:

1461862

Hom.:

Cov.:

AF XY:

0.00988

AC XY:

7187

AN XY:

727230

show subpopulations

Gnomad4 AFR exome

AF:

0.00194

Gnomad4 AMR exome

AF:

0.00452

Gnomad4 ASJ exome

AF:

0.00861

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00922

Gnomad4 FIN exome

AF:

0.0132

Gnomad4 NFE exome

AF:

0.0109

Gnomad4 OTH exome

AF:

0.00897

GnomAD4 genome

AF:

0.00706

AC:

1075

AN:

152324

Hom.:

Cov.:

AF XY:

0.00749

AC XY:

558

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.00147

Gnomad4 AMR

AF:

0.00614

Gnomad4 ASJ

AF:

0.00807

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00872

Gnomad4 FIN

AF:

0.0128

Gnomad4 NFE

AF:

0.0103

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.00922

Hom.:

Bravo

AF:

0.00633

TwinsUK

AF:

0.0102

AC:

ALSPAC

AF:

0.00752

AC:

ESP6500AA

AF:

0.00159

AC:

ESP6500EA

AF:

0.00896

AC:

ExAC

AF:

0.00818

AC:

993

Asia WGS

AF:

0.00462

AC:

AN:

3478

EpiCase

AF:

0.00812

EpiControl

AF:

0.00836

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.53

BayesDel_noAF

Benign

-0.52

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.020

Eigen

Benign

0.18

Eigen_PC

Uncertain

0.27

FATHMM_MKL

Benign

0.44

LIST_S2

Benign

0.77

MetaRNN

Benign

0.0079

MetaSVM

Benign

-0.72

MutationAssessor

Benign

1.6

MutationTaster

Benign

0.99

PrimateAI

Benign

0.43

PROVEAN

Benign

-1.5

REVEL

Benign

0.17

Sift

Benign

0.074

Sift4G

Uncertain

0.029

Polyphen

0.32

Vest4

0.34

MVP

0.61

MPC

0.14

ClinPred

0.029

GERP RS

5.2

Varity_R

0.29

gMVP

0.44

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over