chr15-32758222-C-T

Variant names:

• chr15-32758222-C-T
• rs1258763

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 0.594 in 151,966 control chromosomes in the GnomAD database, including 27,959 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 0.59 (27959 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173
• Publications: 28 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.671 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: 0.594 AC: 90189 AN: 151848 Hom.: 27940 Cov.: 33

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.0760

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.594 AC: 90246 AN: 151966 Hom.: 27959 Cov.: 33 AF XY: 0.589 AC XY: 43741 AN XY: 74286

African (AFR) AF: 0.508 AC: 21084 AN: 41464

American (AMR) AF: 0.654 AC: 9985 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2319 AN: 3472

East Asian (EAS) AF: 0.0765 AC: 396 AN: 5174

South Asian (SAS) AF: 0.483 AC: 2335 AN: 4830

European-Finnish (FIN) AF: 0.574 AC: 6046 AN: 10538

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 45939 AN: 67904

Other (OTH) AF: 0.583 AC: 1229 AN: 2108

Alfa AF: 0.636 Hom.: 68152

Bravo AF: 0.594

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.5
DANN	Benign	0.84
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1258763; hg19: chr15-33050423;