chr10-79999239-A-G

Variant names:

• chr10-79999239-A-G
• rs7904954

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 0.636 in 152,178 control chromosomes in the GnomAD database, including 31,199 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 0.64 (31199 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.763 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: 0.636 AC: 96670 AN: 152060 Hom.: 31153 Cov.: 34

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.636 AC: 96775 AN: 152178 Hom.: 31199 Cov.: 34 AF XY: 0.636 AC XY: 47328 AN XY: 74398

African (AFR) AF: 0.724 AC: 30044 AN: 41510

American (AMR) AF: 0.599 AC: 9149 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2205 AN: 3468

East Asian (EAS) AF: 0.637 AC: 3306 AN: 5188

South Asian (SAS) AF: 0.783 AC: 3779 AN: 4824

European-Finnish (FIN) AF: 0.543 AC: 5740 AN: 10580

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40389 AN: 68004

Other (OTH) AF: 0.631 AC: 1332 AN: 2112

Alfa AF: 0.606 Hom.: 120290

Bravo AF: 0.639

Asia WGS AF: 0.734 AC: 2551 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	1.0
DANN	Benign	0.55
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs7904954; hg19: chr10-81758995;