15-73854903-A-G

Position:

• chr15-73854903-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 0.405 in 152,018 control chromosomes in the GnomAD database, including 13,720 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 0.40 (13720 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61549 AN: 151898 Hom.: 13719 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.0428

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.405 AC: 61560 AN: 152018 Hom.: 13720 Cov.: 32 AF XY: 0.401 AC XY: 29839 AN XY: 74332

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.570

Gnomad4 EAS AF: 0.0429

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.429

Alfa AF: 0.484 Hom.: 37398

Bravo AF: 0.399

Asia WGS AF: 0.178 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.24
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1823718; hg19: chr15-74147244;