rs10492230

Variant names:

• chr12-91186975-G-A
• rs10492230
• ENST00000719112.1:n.203-1265G>A

Variant summary

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

The ENST00000719112.1(ENSG00000293802):​n.203-1265G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 151,928 control chromosomes in the GnomAD database, including 1,455 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 0.12 (1455 hom., cov: 32)
• Consequence: ENSG00000293802 ENST00000719112.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374
• Publications: 4 publications found

Genes affected

ENSG00000293802 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.173 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
ENSG00000293802	ENST00000719112.1	n.203-1265G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18792 AN: 151812 Hom.: 1456 Cov.: 32

Gnomad AFR AF: 0.0560

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0559

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.124 AC: 18794 AN: 151928 Hom.: 1455 Cov.: 32 AF XY: 0.120 AC XY: 8948 AN XY: 74260

African (AFR) AF: 0.0560 AC: 2320 AN: 41464

American (AMR) AF: 0.138 AC: 2099 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 494 AN: 3464

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5176

South Asian (SAS) AF: 0.0557 AC: 268 AN: 4808

European-Finnish (FIN) AF: 0.110 AC: 1162 AN: 10568

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11944 AN: 67922

Other (OTH) AF: 0.145 AC: 305 AN: 2106

Alfa AF: 0.141 Hom.: 263

Bravo AF: 0.123

Asia WGS AF: 0.0320 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.72
DANN	Benign	0.66
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs10492230; hg19: chr12-91580752;