chr15-50547075-G-A

Position:

• chr15-50547075-G-A

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 0.354 in 151,652 control chromosomes in the GnomAD database, including 10,582 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 0.35 (10582 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.475 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: 0.354 AC: 53696 AN: 151536 Hom.: 10582 Cov.: 30

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.354 AC: 53708 AN: 151652 Hom.: 10582 Cov.: 30 AF XY: 0.360 AC XY: 26670 AN XY: 74060

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.406

Alfa AF: 0.365 Hom.: 1334

Bravo AF: 0.355

Asia WGS AF: 0.354 AC: 1227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.9
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3109881; hg19: chr15-50839272;