10-99861014-C-G

Variant names:

• chr10-99861014-C-G
• rs12762549

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 0.468 in 151,492 control chromosomes in the GnomAD database, including 16,751 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 0.47 (16751 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 28 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.555 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: 0.468 AC: 70778 AN: 151374 Hom.: 16735 Cov.: 28

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.468 AC: 70852 AN: 151492 Hom.: 16751 Cov.: 28 AF XY: 0.469 AC XY: 34708 AN XY: 73972

African (AFR) AF: 0.423 AC: 17439 AN: 41244

American (AMR) AF: 0.479 AC: 7277 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1839 AN: 3464

East Asian (EAS) AF: 0.572 AC: 2940 AN: 5140

South Asian (SAS) AF: 0.537 AC: 2573 AN: 4790

European-Finnish (FIN) AF: 0.438 AC: 4580 AN: 10466

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32490 AN: 67882

Other (OTH) AF: 0.491 AC: 1031 AN: 2100

Alfa AF: 0.454 Hom.: 2034

Bravo AF: 0.470

Asia WGS AF: 0.561 AC: 1950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.55
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs12762549; hg19: chr10-101620771;