15-49712620-G-C

Position:

• chr15-49712620-G-C

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 0.293 in 151,918 control chromosomes in the GnomAD database, including 7,070 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 0.29 (7070 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.367 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: 0.293 AC: 44432 AN: 151806 Hom.: 7067 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.293 AC: 44438 AN: 151918 Hom.: 7070 Cov.: 32 AF XY: 0.288 AC XY: 21405 AN XY: 74234

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.295

Alfa AF: 0.188 Hom.: 424

Bravo AF: 0.283

Asia WGS AF: 0.205 AC: 714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7178146; hg19: chr15-50004817;