rs7912580

Positions:

• chr10-62156213-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0199

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.0406

Gnomad4 EAS AF: 0.0599

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.0991

Gnomad4 OTH AF: 0.0649

Alfa AF: 0.0976 Hom.: 412

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7912580; hg19: chr10-63915972;