rs10506643

Variant names:

• chr12-71927834-A-G
• rs10506643

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 0.0912 in 152,188 control chromosomes in the GnomAD database, including 702 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 0.091 (702 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.66

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.135 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: 0.0912 AC: 13871 AN: 152070 Hom.: 700 Cov.: 32

Gnomad AFR AF: 0.0977

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0702

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0765

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0959

Gnomad OTH AF: 0.0919

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

GnomAD4 genome AF: 0.0912 AC: 13885 AN: 152188 Hom.: 702 Cov.: 32 AF XY: 0.0917 AC XY: 6828 AN XY: 74430

Gnomad4 AFR AF: 0.0977

Gnomad4 AMR AF: 0.0701

Gnomad4 ASJ AF: 0.0960

Gnomad4 EAS AF: 0.0214

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0765

Gnomad4 NFE AF: 0.0959

Gnomad4 OTH AF: 0.0956

Alfa AF: 0.104 Hom.: 106

Bravo AF: 0.0872

Asia WGS AF: 0.0980 AC: 342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.4
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10506643; hg19: chr12-72321614;