rs17512051

Variant names:

• chr12-118135862-T-A
• rs17512051
• ENST00000539956.1:n.165A>T

Your query was ambiguous. Multiple possible variants found:

• chr12-118135862-T-A
• chr12-118135862-T-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000539956.1(VSIG10):​n.165A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 271,832 control chromosomes in the GnomAD database, including 2,526 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.13 (1360 hom., cov: 32)
  • Exomes 𝑓: 0.13 (1166 hom.)
• Consequence: VSIG10 ENST00000539956.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238
• Publications: 3 publications found

Genes affected

VSIG10 (HGNC:26078): (V-set and immunoglobulin domain containing 10) 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]

LOC101928274 (HGNC:):

PEBP1 (HGNC:8630): (phosphatidylethanolamine binding protein 1) This gene encodes a member of the phosphatidylethanolamine-binding family of proteins and has been shown to modulate multiple signaling pathways, including the MAP kinase (MAPK), NF-kappa B, and glycogen synthase kinase-3 (GSK-3) signaling pathways. The encoded protein can be further processed to form a smaller cleavage product, hippocampal cholinergic neurostimulating peptide (HCNP), which may be involved in neural development. This gene has been implicated in numerous human cancers and may act as a metastasis suppressor gene. Multiple pseudogenes of this gene have been identified in the genome. [provided by RefSeq, Jul 2015]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000539956.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VSIG10	ENST00000539956.1	TSL:2	n.165A>T		non_coding_transcript_exon	Exon 1 of 4
	VSIG10	ENST00000542011.1	TSL:3	n.87A>T		non_coding_transcript_exon	Exon 1 of 4
	PEBP1	ENST00000874101.1		c.-348T>A		upstream_gene	N/A	ENSP00000544160.1

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19697 AN: 152176 Hom.: 1359 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0977

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.0696

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.113

GnomAD4 exome AF: 0.130 AC: 15516 AN: 119538 Hom.: 1166 Cov.: 0 AF XY: 0.132 AC XY: 8133 AN XY: 61590

African (AFR) AF: 0.0908 AC: 272 AN: 2996

American (AMR) AF: 0.0790 AC: 251 AN: 3178

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 463 AN: 3980

East Asian (EAS) AF: 0.0515 AC: 344 AN: 6674

South Asian (SAS) AF: 0.159 AC: 1635 AN: 10314

European-Finnish (FIN) AF: 0.130 AC: 1210 AN: 9308

Middle Eastern (MID) AF: 0.128 AC: 76 AN: 594

European-Non Finnish (NFE) AF: 0.139 AC: 10369 AN: 74866

Other (OTH) AF: 0.117 AC: 896 AN: 7628

GnomAD4 genome AF: 0.129 AC: 19707 AN: 152294 Hom.: 1360 Cov.: 32 AF XY: 0.130 AC XY: 9651 AN XY: 74464

African (AFR) AF: 0.110 AC: 4571 AN: 41576

American (AMR) AF: 0.0976 AC: 1493 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 411 AN: 3472

East Asian (EAS) AF: 0.0695 AC: 360 AN: 5178

South Asian (SAS) AF: 0.164 AC: 792 AN: 4826

European-Finnish (FIN) AF: 0.145 AC: 1537 AN: 10610

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10187 AN: 68010

Other (OTH) AF: 0.113 AC: 240 AN: 2116

Alfa AF: 0.137 Hom.: 188

Bravo AF: 0.124

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	6.9
DANN	Benign	0.65
PhyloP100		-0.24
PromoterAI		0.0041	Neutral
Mutation Taster		=300/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17512051;

hg19: chr12-118573667;