15-71792354-A-G

Variant names:

• chr15-71792354-A-G
• rs11634405

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.172 AC: 7140 AN: 41494

American (AMR) AF: 0.585 AC: 8937 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2058 AN: 3470

East Asian (EAS) AF: 0.197 AC: 1014 AN: 5154

South Asian (SAS) AF: 0.549 AC: 2636 AN: 4800

European-Finnish (FIN) AF: 0.633 AC: 6684 AN: 10562

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42848 AN: 67932

Other (OTH) AF: 0.493 AC: 1041 AN: 2112

Alfa AF: 0.581 Hom.: 15283

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
PhyloP100		0.20
PromoterAI		0.0022	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11634405; hg19: chr15-72084693;