NM_001365077.2:c.1818C>T

Variant names:

• chr11-125954118-C-T
• rs192608745
• NM_001365077.2:c.1818C>T

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_Moderate BP6_Moderate BP7 BS2

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
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.913
• Publications: 0 publications found

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

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 VariationId 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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001365077.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VSIG10L2	NM_001365077.2	MANE Select	c.1818C>T	p.Ser606Ser	synonymous	Exon 8 of 12	NP_001352006.1	A0A8I5KPR9
	VSIG10L2	NM_001391971.1		c.252C>T	p.Ser84Ser	synonymous	Exon 2 of 4	NP_001378900.1
	VSIG10L2	NM_001391972.1		c.221-1497C>T		intron	N/A	NP_001378901.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VSIG10L2	ENST00000686984.1	MANE Select	c.1818C>T	p.Ser606Ser	synonymous	Exon 8 of 12	ENSP00000509422.1	A0A8I5KPR9
	VSIG10L2	ENST00000638511.1	TSL:1	n.283-1497C>T		intron	N/A
	VSIG10L2	ENST00000638636.2	TSL:5	c.1818C>T	p.Ser606Ser	synonymous	Exon 8 of 10	ENSP00000491467.1	P0DP72

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

African (AFR) AF: 0.00462 AC: 106 AN: 22966

American (AMR) AF: 0.000832 AC: 7 AN: 8418

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 274 AN: 14392

East Asian (EAS) AF: 0.00 AC: 0 AN: 26526

South Asian (SAS) AF: 0.0000513 AC: 1 AN: 19494

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21536

Middle Eastern (MID) AF: 0.00172 AC: 5 AN: 2914

European-Non Finnish (NFE) AF: 0.000105 AC: 97 AN: 920038

Other (OTH) AF: 0.00192 AC: 84 AN: 43680

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

African (AFR) AF: 0.00440 AC: 183 AN: 41562

American (AMR) AF: 0.00118 AC: 18 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.00 AC: 0 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10618

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000176 AC: 12 AN: 68024

Other (OTH) AF: 0.00237 AC: 5 AN: 2108

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00223

Asia WGS AF: 0.00115 AC: 4 AN: 3478

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
CADD	Benign	9.5
DANN	Benign	0.89
PhyloP100		0.91
Mutation Taster		=99/1	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs192608745; hg19: chr11-125824013;