rs12049646

Variant names:

• chr10-67864226-T-C
• rs12049646

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 0.0759 in 152,236 control chromosomes in the GnomAD database, including 725 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 0.076 (725 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 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: 0.0760 AC: 11556 AN: 152116 Hom.: 724 Cov.: 32

Gnomad AFR AF: 0.0269

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0409

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0661

Gnomad OTH AF: 0.0745

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

GnomAD4 genome AF: 0.0759 AC: 11554 AN: 152236 Hom.: 725 Cov.: 32 AF XY: 0.0818 AC XY: 6089 AN XY: 74428

African (AFR) AF: 0.0268 AC: 1115 AN: 41572

American (AMR) AF: 0.118 AC: 1795 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0409 AC: 142 AN: 3472

East Asian (EAS) AF: 0.303 AC: 1564 AN: 5168

South Asian (SAS) AF: 0.130 AC: 624 AN: 4818

European-Finnish (FIN) AF: 0.147 AC: 1561 AN: 10608

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

European-Non Finnish (NFE) AF: 0.0661 AC: 4495 AN: 68012

Other (OTH) AF: 0.0733 AC: 155 AN: 2116

Alfa AF: 0.0672 Hom.: 60

Bravo AF: 0.0733

Asia WGS AF: 0.186 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	10
DANN	Benign	0.79
PhyloP100		-0.097

Splicing

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

Other links and lift over

dbSNP: rs12049646; hg19: chr10-69623984;