chr10-92686366-G-C

Variant names:

• chr10-92686366-G-C
• rs12262390

Variant summary

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

The variant allele was found at a frequency of 0.0874 in 151,318 control chromosomes in the GnomAD database, including 662 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 0.087 (662 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.107 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

Frequencies

GnomAD3 genomes AF: 0.0874 AC: 13219 AN: 151238 Hom.: 662 Cov.: 31

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.0651

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0373

Gnomad FIN AF: 0.0491

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.0878

Gnomad OTH AF: 0.0904

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

GnomAD4 genome AF: 0.0874 AC: 13225 AN: 151318 Hom.: 662 Cov.: 31 AF XY: 0.0833 AC XY: 6157 AN XY: 73882

African (AFR) AF: 0.110 AC: 4526 AN: 41248

American (AMR) AF: 0.0649 AC: 988 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 767 AN: 3468

East Asian (EAS) AF: 0.000774 AC: 4 AN: 5166

South Asian (SAS) AF: 0.0372 AC: 178 AN: 4788

European-Finnish (FIN) AF: 0.0491 AC: 505 AN: 10282

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 290

European-Non Finnish (NFE) AF: 0.0878 AC: 5959 AN: 67862

Other (OTH) AF: 0.0896 AC: 187 AN: 2088

Alfa AF: 0.0939 Hom.: 91

Bravo AF: 0.0905

Asia WGS AF: 0.0280 AC: 100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.6
DANN	Benign	0.86
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs12262390; hg19: chr10-94446123;