10-80007632-A-G

Variant names:

• chr10-80007632-A-G
• rs7070394

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 0.715 in 152,086 control chromosomes in the GnomAD database, including 40,152 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 0.72 (40152 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.907 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: 0.715 AC: 108621 AN: 151968 Hom.: 40078 Cov.: 33

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.715 AC: 108753 AN: 152086 Hom.: 40152 Cov.: 33 AF XY: 0.712 AC XY: 52903 AN XY: 74324

African (AFR) AF: 0.914 AC: 37969 AN: 41520

American (AMR) AF: 0.632 AC: 9654 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 2283 AN: 3472

East Asian (EAS) AF: 0.601 AC: 3115 AN: 5182

South Asian (SAS) AF: 0.777 AC: 3747 AN: 4824

European-Finnish (FIN) AF: 0.592 AC: 6248 AN: 10546

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43418 AN: 67948

Other (OTH) AF: 0.694 AC: 1466 AN: 2112

Alfa AF: 0.657 Hom.: 110188

Bravo AF: 0.721

Asia WGS AF: 0.724 AC: 2518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.57
DANN	Benign	0.46
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs7070394; hg19: chr10-81767388;