Variant 19-51341816-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001163922.3(VSIG10L):c.232T>A(p.Ser78Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00674 in 1,551,516 control chromosomes in the GnomAD database, including 83 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0094 ( 15 hom., cov: 32)

Exomes 𝑓: 0.0065 ( 68 hom. )

Consequence

VSIG10L
NM_001163922.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0270

Variant links:

Genes affected

VSIG10L (HGNC:27111): (V-set and immunoglobulin domain containing 10 like) Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

VSIG10L links:

VSIG10L-AS1 (HGNC:55282): (VSIG10L antisense RNA 1)

VSIG10L-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0020125508).

BP6

Variant 19-51341816-A-T is Benign according to our data. Variant chr19-51341816-A-T is described in ClinVar as [Benign]. Clinvar id is 789497.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00936 (1425/152294) while in subpopulation EAS AF= 0.0402 (208/5174). AF 95% confidence interval is 0.0357. There are 15 homozygotes in gnomad4. There are 732 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 15 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VSIG10L	NM_001163922.3 linkuse as main transcript	c.232T>A	p.Ser78Thr	missense_variant	2/10	ENST00000335624.5	NP_001157394.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VSIG10L	ENST00000335624.5 linkuse as main transcript	c.232T>A	p.Ser78Thr	missense_variant	2/10	5	NM_001163922.3	ENSP00000335623	P1	Q86VR7-1
VSIG10L-AS1	ENST00000594311.1 linkuse as main transcript	n.133-56A>T		intron_variant, non_coding_transcript_variant		5
VSIG10L-AS1	ENST00000601148.5 linkuse as main transcript	n.133-34A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.00938

AC:

1428

AN:

152176

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0143

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0165

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0401

Gnomad SAS

AF:

0.0124

Gnomad FIN

AF:

0.00536

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00345

Gnomad OTH

AF:

0.0100

GnomAD3 exomes

AF:

0.0103

AC:

1581

AN:

153554

Hom.:

AF XY:

0.0101

AC XY:

826

AN XY:

81528

show subpopulations

Gnomad AFR exome

AF:

0.0163

Gnomad AMR exome

AF:

0.0153

Gnomad ASJ exome

AF:

0.000354

Gnomad EAS exome

AF:

0.0403

Gnomad SAS exome

AF:

0.0136

Gnomad FIN exome

AF:

0.00642

Gnomad NFE exome

AF:

0.00333

Gnomad OTH exome

AF:

0.00739

GnomAD4 exome

AF:

0.00645

AC:

9030

AN:

1399222

Hom.:

Cov.:

AF XY:

0.00645

AC XY:

4454

AN XY:

690134

show subpopulations

Gnomad4 AFR exome

AF:

0.0164

Gnomad4 AMR exome

AF:

0.0158

Gnomad4 ASJ exome

AF:

0.000238

Gnomad4 EAS exome

AF:

0.0428

Gnomad4 SAS exome

AF:

0.0111

Gnomad4 FIN exome

AF:

0.00546

Gnomad4 NFE exome

AF:

0.00446

Gnomad4 OTH exome

AF:

0.00771

GnomAD4 genome

AF:

0.00936

AC:

1425

AN:

152294

Hom.:

Cov.:

AF XY:

0.00983

AC XY:

732

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.0143

Gnomad4 AMR

AF:

0.0164

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0402

Gnomad4 SAS

AF:

0.0124

Gnomad4 FIN

AF:

0.00536

Gnomad4 NFE

AF:

0.00345

Gnomad4 OTH

AF:

0.00945

Alfa

AF:

0.00573

Hom.:

Bravo

AF:

0.0111

TwinsUK

AF:

0.00647

AC:

ALSPAC

AF:

0.00493

AC:

ESP6500AA

AF:

0.0130

AC:

ESP6500EA

AF:

0.00251

AC:

ExAC

AF:

0.00804

AC:

180

Asia WGS

AF:

0.0250

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 26, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.097

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.69

CADD

Benign

DANN

Benign

0.89

DEOGEN2

Benign

0.0064

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.069

LIST_S2

Benign

0.35

MetaRNN

Benign

0.0020

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.90

MutationTaster

Benign

1.0

PrimateAI

Benign

0.26

PROVEAN

Benign

-0.79

REVEL

Benign

0.026

Sift

Benign

0.059

Sift4G

Pathogenic

0.0

Polyphen

0.38

Vest4

0.14

ClinPred

0.00063

GERP RS

-2.6

Varity_R

0.058

gMVP

0.16

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