rs12951391

Positions:

• chr17-71915441-C-T

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 0.206 in 151,730 control chromosomes in the GnomAD database, including 3,383 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 0.21 (3383 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31194 AN: 151612 Hom.: 3378 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.0936

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.0166

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.206 AC: 31208 AN: 151730 Hom.: 3383 Cov.: 32 AF XY: 0.204 AC XY: 15121 AN XY: 74112

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.0162

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.194

Alfa AF: 0.210 Hom.: 7215

Bravo AF: 0.199

Asia WGS AF: 0.105 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
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: rs12951391; hg19: chr17-69911582;