12-118135862-T-A

Position:

• chr12-118135862-T-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

VSIG10 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101928274	XR_001749342.3	n.131A>T		non_coding_transcript_exon_variant	1/4
LOC101928274	XR_001749343.3	n.131A>T		non_coding_transcript_exon_variant	1/5
LOC101928274	XR_007063475.1	n.131A>T		non_coding_transcript_exon_variant	1/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VSIG10	ENST00000539956.1	n.165A>T		non_coding_transcript_exon_variant	1/4	2
VSIG10	ENST00000542011.1	n.87A>T		non_coding_transcript_exon_variant	1/4	3

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

Gnomad4 AFR exome AF: 0.0908

Gnomad4 AMR exome AF: 0.0790

Gnomad4 ASJ exome AF: 0.116

Gnomad4 EAS exome AF: 0.0515

Gnomad4 SAS exome AF: 0.159

Gnomad4 FIN exome AF: 0.130

Gnomad4 NFE exome AF: 0.139

Gnomad4 OTH exome AF: 0.117

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

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.0976

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.0695

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.113

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	6.9
DANN	Benign	0.65

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

Other links and lift over

dbSNP: rs17512051; hg19: chr12-118573667;