15-71792354-A-G

Variant names:

• chr15-71792354-A-G
• rs11634405

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 0.48 in 152,018 control chromosomes in the GnomAD database, including 20,898 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 0.48 (20898 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.626 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: 0.481 AC: 73013 AN: 151900 Hom.: 20901 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.480 AC: 73010 AN: 152018 Hom.: 20898 Cov.: 32 AF XY: 0.481 AC XY: 35719 AN XY: 74294

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.493

Alfa AF: 0.578 Hom.: 13788

Bravo AF: 0.461

Asia WGS AF: 0.328 AC: 1144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11634405; hg19: chr15-72084693;