15-34692682-G-C

Variant names:

• chr15-34692682-G-C
• rs1370156

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 0.67 in 151,910 control chromosomes in the GnomAD database, including 34,316 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 0.67 (34316 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.975

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 (SAS) allele frequency at 95% confidence interval = 0.768 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: 0.670 AC: 101683 AN: 151792 Hom.: 34280 Cov.: 31

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.670 AC: 101775 AN: 151910 Hom.: 34316 Cov.: 31 AF XY: 0.673 AC XY: 49963 AN XY: 74230

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.657

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.669

Gnomad4 SAS AF: 0.789

Gnomad4 FIN AF: 0.705

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.653

Alfa AF: 0.558 Hom.: 1727

Bravo AF: 0.666

Asia WGS AF: 0.717 AC: 2495 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	0.31
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1370156; hg19: chr15-34984883;