15-73373165-T-G

Position:

• chr15-73373165-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 0.197 in 152,086 control chromosomes in the GnomAD database, including 3,322 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 0.20 (3322 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.691

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 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: 0.197 AC: 29972 AN: 151968 Hom.: 3304 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.0349

Gnomad SAS AF: 0.0981

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.197 AC: 30030 AN: 152086 Hom.: 3322 Cov.: 31 AF XY: 0.197 AC XY: 14616 AN XY: 74346

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.0348

Gnomad4 SAS AF: 0.0976

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.184

Alfa AF: 0.0846 Hom.: 113

Bravo AF: 0.200

Asia WGS AF: 0.108 AC: 373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.4
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4489968; hg19: chr15-73665506;