rs7912580

Variant names:

• chr10-62156213-G-A
• rs7912580

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 0.0784 in 152,198 control chromosomes in the GnomAD database, including 622 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 0.078 (622 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.216 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: 0.0783 AC: 11906 AN: 152080 Hom.: 611 Cov.: 32

Gnomad AFR AF: 0.0199

Gnomad AMI AF: 0.0453

Gnomad AMR AF: 0.0992

Gnomad ASJ AF: 0.0406

Gnomad EAS AF: 0.0596

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0991

Gnomad OTH AF: 0.0598

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

GnomAD4 genome AF: 0.0784 AC: 11931 AN: 152198 Hom.: 622 Cov.: 32 AF XY: 0.0829 AC XY: 6166 AN XY: 74400

African (AFR) AF: 0.0199 AC: 825 AN: 41544

American (AMR) AF: 0.100 AC: 1528 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0406 AC: 141 AN: 3470

East Asian (EAS) AF: 0.0599 AC: 310 AN: 5176

South Asian (SAS) AF: 0.227 AC: 1096 AN: 4820

European-Finnish (FIN) AF: 0.103 AC: 1093 AN: 10586

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0991 AC: 6741 AN: 68004

Other (OTH) AF: 0.0649 AC: 137 AN: 2112

Alfa AF: 0.0893 Hom.: 1403

Bravo AF: 0.0693

Asia WGS AF: 0.150 AC: 520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs7912580; hg19: chr10-63915972;