10-92760912-C-T

Variant names:

• chr10-92760912-C-T
• rs10509646

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 0.446 in 151,114 control chromosomes in the GnomAD database, including 15,841 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 0.45 (15841 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168
• Publications: 5 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 = 0.828 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: 0.446 AC: 67312 AN: 150994 Hom.: 15823 Cov.: 29

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.446 AC: 67366 AN: 151114 Hom.: 15841 Cov.: 29 AF XY: 0.452 AC XY: 33338 AN XY: 73762

African (AFR) AF: 0.344 AC: 14161 AN: 41160

American (AMR) AF: 0.477 AC: 7228 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1640 AN: 3464

East Asian (EAS) AF: 0.849 AC: 4352 AN: 5124

South Asian (SAS) AF: 0.601 AC: 2876 AN: 4784

European-Finnish (FIN) AF: 0.446 AC: 4588 AN: 10276

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31207 AN: 67840

Other (OTH) AF: 0.465 AC: 977 AN: 2102

Alfa AF: 0.446 Hom.: 12378

Bravo AF: 0.443

Asia WGS AF: 0.703 AC: 2443 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	3.9
DANN	Benign	0.78
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs10509646; hg19: chr10-94520669;