rs10512056

Variant names:

• chr9-76990670-A-T
• rs10512056

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 0.397 in 149,226 control chromosomes in the GnomAD database, including 11,942 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 0.40 (11942 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.548
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 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: 0.397 AC: 59203 AN: 149110 Hom.: 11926 Cov.: 25

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.406

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.397 AC: 59270 AN: 149226 Hom.: 11942 Cov.: 25 AF XY: 0.399 AC XY: 29009 AN XY: 72732

African (AFR) AF: 0.424 AC: 17046 AN: 40240

American (AMR) AF: 0.411 AC: 6146 AN: 14946

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1655 AN: 3448

East Asian (EAS) AF: 0.441 AC: 2193 AN: 4972

South Asian (SAS) AF: 0.359 AC: 1686 AN: 4702

European-Finnish (FIN) AF: 0.370 AC: 3746 AN: 10132

Middle Eastern (MID) AF: 0.424 AC: 122 AN: 288

European-Non Finnish (NFE) AF: 0.378 AC: 25498 AN: 67518

Other (OTH) AF: 0.424 AC: 881 AN: 2076

Alfa AF: 0.392 Hom.: 1437

Bravo AF: 0.409

Asia WGS AF: 0.396 AC: 1377 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	7.5
DANN	Benign	0.64
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs10512056; hg19: chr9-79605586; COSMIC: COSV71589775;