chr15-32702555-T-C

Variant names:

• chr15-32702555-T-C
• rs4779584

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 0.668 in 152,122 control chromosomes in the GnomAD database, including 36,462 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 0.67 (36462 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204
• Publications: 173 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.801 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: 0.668 AC: 101515 AN: 152004 Hom.: 36436 Cov.: 33

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.668 AC: 101591 AN: 152122 Hom.: 36462 Cov.: 33 AF XY: 0.663 AC XY: 49285 AN XY: 74356

African (AFR) AF: 0.447 AC: 18535 AN: 41486

American (AMR) AF: 0.733 AC: 11213 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.874 AC: 3033 AN: 3470

East Asian (EAS) AF: 0.194 AC: 1002 AN: 5176

South Asian (SAS) AF: 0.593 AC: 2858 AN: 4820

European-Finnish (FIN) AF: 0.716 AC: 7560 AN: 10562

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.806 AC: 54841 AN: 68000

Other (OTH) AF: 0.707 AC: 1496 AN: 2116

Alfa AF: 0.754 Hom.: 162475

Bravo AF: 0.662

Asia WGS AF: 0.419 AC: 1460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.1
DANN	Benign	0.74
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs4779584; hg19: chr15-32994756;