rs1391681

Variant names:

• chr12-102972207-C-A
• rs1391681

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 0.532 in 152,104 control chromosomes in the GnomAD database, including 24,434 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 0.53 (24434 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

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 (EAS) allele frequency at 95% confidence interval = 0.849 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: 0.532 AC: 80893 AN: 151986 Hom.: 24425 Cov.: 34

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.532 AC: 80923 AN: 152104 Hom.: 24434 Cov.: 34 AF XY: 0.541 AC XY: 40209 AN XY: 74352

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.870

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.563

Alfa AF: 0.586 Hom.: 4787

Bravo AF: 0.515

Asia WGS AF: 0.775 AC: 2694 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	5.0
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1391681; hg19: chr12-103365985;