chr15-74735539-C-T

Variant names:

• chr15-74735539-C-T
• rs2472297

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 0.152 in 152,072 control chromosomes in the GnomAD database, including 2,566 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 0.15 (2566 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.748
• Publications: 161 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.239 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: 0.152 AC: 23127 AN: 151954 Hom.: 2568 Cov.: 32

Gnomad AFR AF: 0.0419

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0955

Gnomad ASJ AF: 0.0792

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0358

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.152 AC: 23124 AN: 152072 Hom.: 2566 Cov.: 32 AF XY: 0.147 AC XY: 10963 AN XY: 74330

African (AFR) AF: 0.0417 AC: 1733 AN: 41510

American (AMR) AF: 0.0954 AC: 1458 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0792 AC: 275 AN: 3472

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5176

South Asian (SAS) AF: 0.0358 AC: 173 AN: 4830

European-Finnish (FIN) AF: 0.249 AC: 2625 AN: 10540

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16484 AN: 67954

Other (OTH) AF: 0.127 AC: 268 AN: 2106

Alfa AF: 0.190 Hom.: 10859

Bravo AF: 0.137

Asia WGS AF: 0.0190 AC: 68 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.54
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs2472297; hg19: chr15-75027880;