rs627566

Variant names:

• chr15-49760157-C-T
• rs627566

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 0.386 in 151,484 control chromosomes in the GnomAD database, including 11,477 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 0.39 (11477 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510
• Publications: 3 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 = 0.424 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: 0.386 AC: 58433 AN: 151364 Hom.: 11481 Cov.: 31

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.386 AC: 58442 AN: 151484 Hom.: 11477 Cov.: 31 AF XY: 0.386 AC XY: 28533 AN XY: 73998

African (AFR) AF: 0.317 AC: 13112 AN: 41326

American (AMR) AF: 0.366 AC: 5560 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1788 AN: 3456

East Asian (EAS) AF: 0.321 AC: 1644 AN: 5122

South Asian (SAS) AF: 0.340 AC: 1633 AN: 4804

European-Finnish (FIN) AF: 0.429 AC: 4508 AN: 10512

Middle Eastern (MID) AF: 0.483 AC: 141 AN: 292

European-Non Finnish (NFE) AF: 0.428 AC: 29016 AN: 67774

Other (OTH) AF: 0.384 AC: 809 AN: 2106

Alfa AF: 0.417 Hom.: 51340

Bravo AF: 0.380

Asia WGS AF: 0.318 AC: 1109 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	3.2
DANN	Benign	0.59
PhyloP100		0.051

Splicing

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

Other links and lift over

dbSNP: rs627566; hg19: chr15-50052354;