15-45328787-C-T

Variant names:

• chr15-45328787-C-T
• rs1719247

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 0.432 in 151,560 control chromosomes in the GnomAD database, including 17,511 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 0.43 (17511 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940
• Publications: 34 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.814 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: 0.431 AC: 65317 AN: 151442 Hom.: 17449 Cov.: 30

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.432 AC: 65436 AN: 151560 Hom.: 17511 Cov.: 30 AF XY: 0.437 AC XY: 32331 AN XY: 74018

African (AFR) AF: 0.703 AC: 29025 AN: 41266

American (AMR) AF: 0.498 AC: 7580 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1125 AN: 3468

East Asian (EAS) AF: 0.835 AC: 4279 AN: 5126

South Asian (SAS) AF: 0.395 AC: 1896 AN: 4800

European-Finnish (FIN) AF: 0.308 AC: 3223 AN: 10460

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.253 AC: 17177 AN: 67914

Other (OTH) AF: 0.422 AC: 889 AN: 2106

Alfa AF: 0.340 Hom.: 22801

Bravo AF: 0.464

Asia WGS AF: 0.610 AC: 2119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.65
PhyloP100		0.094

Splicing

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

Other links and lift over

dbSNP: rs1719247; hg19: chr15-45620985;