chr15-49715528-A-G

Variant names:

• chr15-49715528-A-G
• rs585451

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 0.327 in 152,082 control chromosomes in the GnomAD database, including 8,949 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 0.33 (8949 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.722
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.389 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: 0.327 AC: 49700 AN: 151964 Hom.: 8954 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.327 AC: 49720 AN: 152082 Hom.: 8949 Cov.: 32 AF XY: 0.329 AC XY: 24434 AN XY: 74336

African (AFR) AF: 0.199 AC: 8239 AN: 41482

American (AMR) AF: 0.348 AC: 5325 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1432 AN: 3470

East Asian (EAS) AF: 0.141 AC: 728 AN: 5174

South Asian (SAS) AF: 0.204 AC: 985 AN: 4818

European-Finnish (FIN) AF: 0.470 AC: 4964 AN: 10560

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26703 AN: 67970

Other (OTH) AF: 0.352 AC: 745 AN: 2114

Alfa AF: 0.367 Hom.: 14230

Bravo AF: 0.313

Asia WGS AF: 0.208 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	14
DANN	Benign	0.94
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs585451; hg19: chr15-50007725;