10-36819307-T-A

Variant names:

• chr10-36819307-T-A
• rs2463226

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 0.547 in 152,002 control chromosomes in the GnomAD database, including 23,053 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 0.55 (23053 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 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: 0.547 AC: 83068 AN: 151884 Hom.: 23030 Cov.: 33

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.547 AC: 83123 AN: 152002 Hom.: 23053 Cov.: 33 AF XY: 0.551 AC XY: 40920 AN XY: 74282

African (AFR) AF: 0.541 AC: 22427 AN: 41458

American (AMR) AF: 0.559 AC: 8535 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1818 AN: 3464

East Asian (EAS) AF: 0.784 AC: 4051 AN: 5166

South Asian (SAS) AF: 0.722 AC: 3482 AN: 4822

European-Finnish (FIN) AF: 0.523 AC: 5522 AN: 10560

Middle Eastern (MID) AF: 0.579 AC: 169 AN: 292

European-Non Finnish (NFE) AF: 0.524 AC: 35618 AN: 67966

Other (OTH) AF: 0.534 AC: 1124 AN: 2106

Alfa AF: 0.523 Hom.: 2497

Bravo AF: 0.549

Asia WGS AF: 0.737 AC: 2550 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.33
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs2463226; hg19: chr10-37108235;