Variant 6-31707506-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_001003693.3(LY6G6F):c.101C>A(p.Pro34Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00353 in 1,614,166 control chromosomes in the GnomAD database, including 101 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.0091 ( 18 hom., cov: 32)

Exomes 𝑓: 0.0030 ( 83 hom. )

Consequence

LY6G6F
NM_001003693.3 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.60

Variant links:

Genes affected

LY6G6F (HGNC:13933): (lymphocyte antigen 6 family member G6F) The human G6f protein is a type I transmembrane protein belonging to the immunoglobin (Ig) superfamily, which is comprised of cell-surface proteins involved in the immune system and cellular recognition (de Vet et al., 2003 [PubMed 12852788]).[supplied by OMIM, Mar 2008]

LY6G6F links:

LY6G6F-LY6G6D (HGNC:):

LY6G6F-LY6G6D links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.010085255).

BP6

Variant 6-31707506-C-A is Benign according to our data. Variant chr6-31707506-C-A is described in ClinVar as [Benign]. Clinvar id is 780983.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00905 (1379/152306) while in subpopulation AFR AF= 0.0272 (1129/41548). AF 95% confidence interval is 0.0259. There are 18 homozygotes in gnomad4. There are 664 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 18 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LY6G6F	NM_001003693.3 linkuse as main transcript	c.101C>A	p.Pro34Gln	missense_variant	2/6	ENST00000375832.5
LY6G6F-LY6G6D	NM_001353334.2 linkuse as main transcript	c.101C>A	p.Pro34Gln	missense_variant	2/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LY6G6F	ENST00000375832.5 linkuse as main transcript	c.101C>A	p.Pro34Gln	missense_variant	2/6	1	NM_001003693.3	P1	Q5SQ64-1

Frequencies

GnomAD3 genomes

AF:

0.00904

AC:

1376

AN:

152188

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0272

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00419

Gnomad ASJ

AF:

0.00346

Gnomad EAS

AF:

0.0129

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.0000941

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00109

Gnomad OTH

AF:

0.0105

GnomAD3 exomes

AF:

0.00439

AC:

1103

AN:

251222

Hom.:

AF XY:

0.00360

AC XY:

489

AN XY:

135812

show subpopulations

Gnomad AFR exome

AF:

0.0318

Gnomad AMR exome

AF:

0.00448

Gnomad ASJ exome

AF:

0.00179

Gnomad EAS exome

AF:

0.0110

Gnomad SAS exome

AF:

0.00160

Gnomad FIN exome

AF:

0.0000462

Gnomad NFE exome

AF:

0.00125

Gnomad OTH exome

AF:

0.00310

GnomAD4 exome

AF:

0.00296

AC:

4320

AN:

1461860

Hom.:

Cov.:

AF XY:

0.00282

AC XY:

2053

AN XY:

727224

show subpopulations

Gnomad4 AFR exome

AF:

0.0314

Gnomad4 AMR exome

AF:

0.00420

Gnomad4 ASJ exome

AF:

0.00222

Gnomad4 EAS exome

AF:

0.0434

Gnomad4 SAS exome

AF:

0.00183

Gnomad4 FIN exome

AF:

0.0000749

Gnomad4 NFE exome

AF:

0.000807

Gnomad4 OTH exome

AF:

0.00311

GnomAD4 genome

AF:

0.00905

AC:

1379

AN:

152306

Hom.:

Cov.:

AF XY:

0.00892

AC XY:

664

AN XY:

74476

show subpopulations

Gnomad4 AFR

AF:

0.0272

Gnomad4 AMR

AF:

0.00418

Gnomad4 ASJ

AF:

0.00346

Gnomad4 EAS

AF:

0.0129

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.0000941

Gnomad4 NFE

AF:

0.00109

Gnomad4 OTH

AF:

0.0104

Alfa

AF:

0.00369

Hom.:

Bravo

AF:

0.0101

TwinsUK

AF:

0.000809

AC:

ALSPAC

AF:

0.000778

AC:

ESP6500AA

AF:

0.0325

AC:

143

ESP6500EA

AF:

0.000581

AC:

ExAC

AF:

0.00501

AC:

608

Asia WGS

AF:

0.0110

AC:

AN:

3478

EpiCase

AF:

0.00174

EpiControl

AF:

0.00207

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

Labcorp Genetics (formerly Invitae), Labcorp

Feb 20, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.34

BayesDel_addAF

Benign

-0.39

BayesDel_noAF

Benign

-0.31

CADD

Uncertain

DANN

Benign

0.97

DEOGEN2

Benign

0.042

T;.

Eigen

Uncertain

0.56

Eigen_PC

Uncertain

0.52

FATHMM_MKL

Uncertain

0.92

LIST_S2

Benign

0.61

T;.

MetaRNN

Benign

0.010

T;T

MetaSVM

Benign

-0.60

MutationAssessor

Uncertain

2.2

M;.

MutationTaster

Benign

0.94

N;N

PrimateAI

Benign

0.42

PROVEAN

Pathogenic

-5.2

D;D

REVEL

Benign

0.14

Sift

Uncertain

0.0030

D;D

Sift4G

Uncertain

0.0090

D;D

Polyphen

0.99

D;.

Vest4

0.53

MVP

0.80

MPC

0.41

ClinPred

0.033

GERP RS

4.8

Varity_R

0.14

gMVP

0.39

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