15-49712620-G-C

Variant names:

• chr15-49712620-G-C
• rs7178146

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.183 AC: 7566 AN: 41430

American (AMR) AF: 0.266 AC: 4070 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1240 AN: 3468

East Asian (EAS) AF: 0.193 AC: 991 AN: 5148

South Asian (SAS) AF: 0.232 AC: 1115 AN: 4816

European-Finnish (FIN) AF: 0.294 AC: 3099 AN: 10540

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25192 AN: 67918

Other (OTH) AF: 0.295 AC: 621 AN: 2106

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
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs7178146; hg19: chr15-50004817;