10-96761759-C-T

Variant names:

• chr10-96761759-C-T
• rs505010

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 0.666 in 152,036 control chromosomes in the GnomAD database, including 35,804 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 0.67 (35804 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 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: 0.666 AC: 101195 AN: 151918 Hom.: 35742 Cov.: 31

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.666 AC: 101319 AN: 152036 Hom.: 35804 Cov.: 31 AF XY: 0.672 AC XY: 49911 AN XY: 74296

African (AFR) AF: 0.873 AC: 36226 AN: 41508

American (AMR) AF: 0.703 AC: 10733 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2053 AN: 3470

East Asian (EAS) AF: 0.961 AC: 4973 AN: 5176

South Asian (SAS) AF: 0.756 AC: 3645 AN: 4824

European-Finnish (FIN) AF: 0.511 AC: 5370 AN: 10516

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36381 AN: 67960

Other (OTH) AF: 0.664 AC: 1402 AN: 2112

Alfa AF: 0.576 Hom.: 51978

Bravo AF: 0.691

Asia WGS AF: 0.855 AC: 2972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.3
DANN	Benign	0.36
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs505010; hg19: chr10-98521516;