15-73720096-A-G

Position:

• chr15-73720096-A-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 0.828 in 152,196 control chromosomes in the GnomAD database, including 52,670 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 0.83 (52670 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.630

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.887 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: 0.828 AC: 125991 AN: 152076 Hom.: 52644 Cov.: 33

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.828 AC: 126073 AN: 152196 Hom.: 52670 Cov.: 33 AF XY: 0.824 AC XY: 61348 AN XY: 74430

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.841

Gnomad4 ASJ AF: 0.917

Gnomad4 EAS AF: 0.639

Gnomad4 SAS AF: 0.750

Gnomad4 FIN AF: 0.858

Gnomad4 NFE AF: 0.893

Gnomad4 OTH AF: 0.858

Alfa AF: 0.878 Hom.: 113204

Bravo AF: 0.823

Asia WGS AF: 0.716 AC: 2487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1038094; hg19: chr15-74012437;