10-67788537-T-A

Variant names:

• chr10-67788537-T-A
• rs10762179

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 0.742 in 139,644 control chromosomes in the GnomAD database, including 36,623 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 0.74 (36623 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.742 AC: 103551 AN: 139536 Hom.: 36630 Cov.: 31

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.876

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.742 AC: 103583 AN: 139644 Hom.: 36623 Cov.: 31 AF XY: 0.741 AC XY: 50549 AN XY: 68258

African (AFR) AF: 0.593 AC: 20443 AN: 34470

American (AMR) AF: 0.761 AC: 10909 AN: 14332

Ashkenazi Jewish (ASJ) AF: 0.844 AC: 2865 AN: 3394

East Asian (EAS) AF: 0.604 AC: 2461 AN: 4072

South Asian (SAS) AF: 0.785 AC: 3507 AN: 4470

European-Finnish (FIN) AF: 0.792 AC: 7999 AN: 10106

Middle Eastern (MID) AF: 0.863 AC: 252 AN: 292

European-Non Finnish (NFE) AF: 0.806 AC: 52875 AN: 65626

Other (OTH) AF: 0.770 AC: 1537 AN: 1996

Alfa AF: 0.715 Hom.: 4894

Bravo AF: 0.668

Asia WGS AF: 0.634 AC: 2203 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.7
DANN	Benign	0.67
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs10762179; hg19: chr10-69548295;