rs1912967

chr15-70290997-T-Achr15-70290997-T-G

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 0.609 in 152,132 control chromosomes in the GnomAD database, including 29,960 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 0.61 (29960 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

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 (NFE) allele frequency at 95% confidence interval = 0.722 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: 0.609 AC: 92543 AN: 152014 Hom.: 29957 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.609 AC: 92576 AN: 152132 Hom.: 29960 Cov.: 32 AF XY: 0.610 AC XY: 45381 AN XY: 74404

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.804

Gnomad4 NFE AF: 0.727

Gnomad4 OTH AF: 0.593

Alfa AF: 0.667 Hom.: 4388

Bravo AF: 0.582

Asia WGS AF: 0.487 AC: 1697 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	0.24
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1912967; hg19: chr15-70583336;