rs12262390

chr10-92686366-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.0649

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.000774

Gnomad4 SAS AF: 0.0372

Gnomad4 FIN AF: 0.0491

Gnomad4 NFE AF: 0.0878

Gnomad4 OTH AF: 0.0896

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12262390; hg19: chr10-94446123;