rs7959363

Variant names:

• chr12-124624381-A-G
• rs7959363

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 0.0866 in 152,246 control chromosomes in the GnomAD database, including 676 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 0.087 (676 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.344

ACMG classification

Verdict is Benign. Variant got -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 = 0.141 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: 0.0866 AC: 13172 AN: 152128 Hom.: 677 Cov.: 33

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0512

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.0696

Gnomad SAS AF: 0.0738

Gnomad FIN AF: 0.0585

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0695

Gnomad OTH AF: 0.0742

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

GnomAD4 genome AF: 0.0866 AC: 13189 AN: 152246 Hom.: 676 Cov.: 33 AF XY: 0.0843 AC XY: 6277 AN XY: 74448

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.0511

Gnomad4 ASJ AF: 0.0395

Gnomad4 EAS AF: 0.0694

Gnomad4 SAS AF: 0.0739

Gnomad4 FIN AF: 0.0585

Gnomad4 NFE AF: 0.0695

Gnomad4 OTH AF: 0.0791

Alfa AF: 0.0730 Hom.: 499

Bravo AF: 0.0877

Asia WGS AF: 0.0700 AC: 244 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	0.83
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7959363; hg19: chr12-125108927;