15-32751254-C-T

Variant names:

• chr15-32751254-C-T
• rs1919360

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 0.196 in 152,076 control chromosomes in the GnomAD database, including 3,465 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 0.20 (3465 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920
• Publications: 6 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 = 0.557 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: 0.196 AC: 29785 AN: 151960 Hom.: 3460 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.196 AC: 29799 AN: 152076 Hom.: 3465 Cov.: 32 AF XY: 0.202 AC XY: 15003 AN XY: 74334

African (AFR) AF: 0.147 AC: 6084 AN: 41468

American (AMR) AF: 0.192 AC: 2944 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 582 AN: 3470

East Asian (EAS) AF: 0.575 AC: 2955 AN: 5142

South Asian (SAS) AF: 0.325 AC: 1567 AN: 4822

European-Finnish (FIN) AF: 0.274 AC: 2898 AN: 10562

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.179 AC: 12187 AN: 68008

Other (OTH) AF: 0.212 AC: 447 AN: 2106

Alfa AF: 0.183 Hom.: 7876

Bravo AF: 0.189

Asia WGS AF: 0.413 AC: 1432 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	1.6
DANN	Benign	0.25
PhyloP100		0.092

Splicing

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

Other links and lift over

dbSNP: rs1919360; hg19: chr15-33043455;