rs1971791

Variant names:

• chr15-70283799-G-A
• rs1971791

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 0.454 in 152,180 control chromosomes in the GnomAD database, including 16,595 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 0.45 (16595 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.893

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.524 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: 0.455 AC: 69126 AN: 152062 Hom.: 16589 Cov.: 33

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.454 AC: 69141 AN: 152180 Hom.: 16595 Cov.: 33 AF XY: 0.457 AC XY: 33981 AN XY: 74406

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.528

Gnomad4 OTH AF: 0.451

Alfa AF: 0.510 Hom.: 42222

Bravo AF: 0.439

Asia WGS AF: 0.417 AC: 1450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1971791; hg19: chr15-70576138;