rs12941471

Variant names:

• chr17-71243794-G-A
• rs12941471

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 0.0868 in 152,228 control chromosomes in the GnomAD database, including 759 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 (759 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.531

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.245 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: 0.0869 AC: 13214 AN: 152110 Hom.: 759 Cov.: 33

Gnomad AFR AF: 0.0439

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.0854

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.0837

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.0740

Gnomad OTH AF: 0.0923

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

GnomAD4 genome AF: 0.0868 AC: 13219 AN: 152228 Hom.: 759 Cov.: 33 AF XY: 0.0922 AC XY: 6864 AN XY: 74430

Gnomad4 AFR AF: 0.0438

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.0854

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.0834

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.0740

Gnomad4 OTH AF: 0.0927

Alfa AF: 0.0746 Hom.: 57

Bravo AF: 0.0912

Asia WGS AF: 0.147 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12941471; hg19: chr17-69239935;