15-49084694-G-C

Variant names:

• chr15-49084694-G-C
• rs17393761

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 0.306 in 151,962 control chromosomes in the GnomAD database, including 8,992 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 0.31 (8992 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.107
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.426 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: 0.307 AC: 46560 AN: 151844 Hom.: 8991 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.306 AC: 46551 AN: 151962 Hom.: 8992 Cov.: 32 AF XY: 0.305 AC XY: 22630 AN XY: 74266

African (AFR) AF: 0.102 AC: 4209 AN: 41460

American (AMR) AF: 0.282 AC: 4304 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1571 AN: 3464

East Asian (EAS) AF: 0.118 AC: 609 AN: 5180

South Asian (SAS) AF: 0.185 AC: 893 AN: 4824

European-Finnish (FIN) AF: 0.435 AC: 4588 AN: 10536

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.430 AC: 29202 AN: 67942

Other (OTH) AF: 0.308 AC: 650 AN: 2110

Alfa AF: 0.253 Hom.: 712

Bravo AF: 0.287

Asia WGS AF: 0.164 AC: 571 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	13
DANN	Benign	0.73
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs17393761; hg19: chr15-49376891;