10-92677094-T-C

Variant names:

• chr10-92677094-T-C
• rs7911264

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 0.529 in 151,278 control chromosomes in the GnomAD database, including 21,471 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 0.53 (21471 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 48 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 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: 0.529 AC: 79964 AN: 151160 Hom.: 21459 Cov.: 29

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.529 AC: 80016 AN: 151278 Hom.: 21471 Cov.: 29 AF XY: 0.527 AC XY: 38893 AN XY: 73824

African (AFR) AF: 0.525 AC: 21606 AN: 41150

American (AMR) AF: 0.471 AC: 7140 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2059 AN: 3468

East Asian (EAS) AF: 0.757 AC: 3897 AN: 5146

South Asian (SAS) AF: 0.564 AC: 2709 AN: 4804

European-Finnish (FIN) AF: 0.526 AC: 5473 AN: 10400

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.520 AC: 35258 AN: 67860

Other (OTH) AF: 0.513 AC: 1077 AN: 2100

Alfa AF: 0.527 Hom.: 31847

Bravo AF: 0.526

Asia WGS AF: 0.622 AC: 2163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	12
DANN	Benign	0.90
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs7911264; hg19: chr10-94436851;