11-125954118-C-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_Moderate BP6_Moderate BP7

The NM_001365077.2(VSIG10L2):c.1818C>T(p.Ser606=) 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
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.913

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]

ACMG classification

Verdict is Likely_benign. Variant got -5 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VSIG10L2	NM_001365077.2	c.1818C>T	p.Ser606=	synonymous_variant	8/12	ENST00000686984.1
VSIG10L2	NM_001391971.1	c.252C>T	p.Ser84=	synonymous_variant	2/4
VSIG10L2	NM_001391972.1	c.221-1497C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VSIG10L2	ENST00000686984.1	c.1818C>T	p.Ser606=	synonymous_variant	8/12		NM_001365077.2	P2
VSIG10L2	ENST00000638511.1	n.283-1497C>T		intron_variant, non_coding_transcript_variant		1
VSIG10L2	ENST00000638636.2	c.1818C>T	p.Ser606=	synonymous_variant	8/10	5		A2
VSIG10L2	ENST00000640497.1	c.240C>T	p.Ser80=	synonymous_variant	2/4	3

Frequencies

GnomAD3 genomes AF: 0.00183 AC: 279 AN: 152180 Hom.: 1 Cov.: 32

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.: 6 Cov.: 31 AF XY: 0.000539 AC XY: 275 AN XY: 509864

Gnomad4 AFR exome AF: 0.00462

Gnomad4 AMR exome AF: 0.000832

Gnomad4 ASJ exome AF: 0.0190

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000513

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000105

Gnomad4 OTH exome AF: 0.00192

GnomAD4 genome AF: 0.00183 AC: 278 AN: 152298 Hom.: 1 Cov.: 32 AF XY: 0.00180 AC XY: 134 AN XY: 74464

Gnomad4 AFR AF: 0.00440

Gnomad4 AMR AF: 0.00118

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000176

Gnomad4 OTH AF: 0.00237

Bravo AF: 0.00223

Asia WGS AF: 0.00115 AC: 4 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2023

VSIG10L2: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
Cadd	Benign	9.5
Dann	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs192608745; hg19: chr11-125824013;