Genetic Variant VSIG10L2:p.Ser606Ser (chr11-125954118-C-T) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_001365077.2(VSIG10L2):c.1818C>T(p.Ser606Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000691 in 1,232,262 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0018 ( 1 hom., cov: 32)

Exomes 𝑓: 0.00053 ( 6 hom. )

Consequence

VSIG10L2
NM_001365077.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.913

Publications

0 publications found

Variant links:

Genes affected

VSIG10L2 (HGNC:27879): (V-set and immunoglobulin domain containing 10 like 2) Predicted to enable cell adhesion molecule binding activity. Predicted to be involved in cell-cell adhesion. Predicted to be active in cell-cell junction. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

VSIG10L2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.2).

BP6

Variant 11-125954118-C-T is Benign according to our data. Variant chr11-125954118-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2642514.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.913 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein
VSIG10L2	NM_001365077.2 link	c.1818C>T	p.Ser606Ser	synonymous_variant	Exon 8 of 12	ENST00000686984.1	NP_001352006.1
VSIG10L2	NM_001391971.1 link	c.252C>T	p.Ser84Ser	synonymous_variant	Exon 2 of 4		NP_001378900.1
VSIG10L2	NM_001391972.1 link	c.221-1497C>T		intron_variant	Intron 1 of 2		NP_001378901.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
VSIG10L2	ENST00000686984.1 link	c.1818C>T	p.Ser606Ser	synonymous_variant	Exon 8 of 12		NM_001365077.2	ENSP00000509422.1	A0A8I5KPR9
VSIG10L2	ENST00000638511.1 link	n.283-1497C>T		intron_variant	Intron 1 of 2	1
VSIG10L2	ENST00000638636.2 link	c.1818C>T	p.Ser606Ser	synonymous_variant	Exon 8 of 10	5		ENSP00000491467.1	P0DP72
VSIG10L2	ENST00000640497.1 link	c.240C>T	p.Ser80Ser	synonymous_variant	Exon 2 of 4	3		ENSP00000491366.1	A0A1W2PP72

Frequencies

GnomAD3 genomes

AF:

0.00183

AC:

279

AN:

152180

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00442

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00118

Gnomad ASJ

AF:

0.0173

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000176

Gnomad OTH

AF:

0.00240

GnomAD4 exome

AF:

0.000531

AC:

574

AN:

1079964

Hom.:

Cov.:

AF XY:

0.000539

AC XY:

275

AN XY:

509864

show subpopulations

African (AFR)

AF:

0.00462

AC:

106

AN:

22966

American (AMR)

AF:

0.000832

AC:

AN:

8418

Ashkenazi Jewish (ASJ)

AF:

0.0190

AC:

274

AN:

14392

East Asian (EAS)

AF:

0.00

AC:

AN:

26526

South Asian (SAS)

AF:

0.0000513

AC:

AN:

19494

European-Finnish (FIN)

AF:

0.00

AC:

AN:

21536

Middle Eastern (MID)

AF:

0.00172

AC:

AN:

2914

European-Non Finnish (NFE)

AF:

0.000105

AC:

AN:

920038

Other (OTH)

AF:

0.00192

AC:

AN:

43680

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

109

146

182

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.00183

AC:

278

AN:

152298

Hom.:

Cov.:

AF XY:

0.00180

AC XY:

134

AN XY:

74464

show subpopulations

African (AFR)

AF:

0.00440

AC:

183

AN:

41562

American (AMR)

AF:

0.00118

AC:

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.0173

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5174

South Asian (SAS)

AF:

0.00

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10618

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000176

AC:

AN:

68024

Other (OTH)

AF:

0.00237

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00223

Asia WGS

AF:

0.00115

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Apr 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

VSIG10L2: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.20

CADD

Benign

9.5

(source)

DANN

Benign

0.89

PhyloP100

0.91

Mutation Taster

=99/1

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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11-125954118-C-T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over