rs12492095

Variant names:

• chr3-124729109-T-A
• rs12492095
• ENST00000683807.1:n.78+1236A>T

Variant summary

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

The ENST00000683807.1(ENSG00000288713):​n.78+1236A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,222 control chromosomes in the GnomAD database, including 2,464 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 0.17 (2464 hom., cov: 31)
• Consequence: ENSG00000288713 ENST00000683807.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545
• Publications: 6 publications found

Genes affected

ENSG00000288713 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288713	ENST00000683807.1	n.78+1236A>T		intron_variant	Intron 1 of 2
ENSG00000288713	ENST00000774319.1	n.114+150A>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26178 AN: 152104 Hom.: 2461 Cov.: 31

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.0993

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.170

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.172 AC: 26191 AN: 152222 Hom.: 2464 Cov.: 31 AF XY: 0.175 AC XY: 13009 AN XY: 74426

African (AFR) AF: 0.139 AC: 5784 AN: 41542

American (AMR) AF: 0.253 AC: 3875 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0993 AC: 344 AN: 3464

East Asian (EAS) AF: 0.180 AC: 932 AN: 5176

South Asian (SAS) AF: 0.203 AC: 979 AN: 4822

European-Finnish (FIN) AF: 0.200 AC: 2124 AN: 10594

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11596 AN: 68014

Other (OTH) AF: 0.171 AC: 362 AN: 2112

Alfa AF: 0.165 Hom.: 278

Bravo AF: 0.174

Asia WGS AF: 0.188 AC: 654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.71
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs12492095; hg19: chr3-124447956;