15-74727108-C-T

Variant names:

• chr15-74727108-C-T
• rs2470893

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 0.195 in 152,142 control chromosomes in the GnomAD database, including 4,067 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 (4067 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579
• Publications: 106 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.306 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: 0.195 AC: 29674 AN: 152024 Hom.: 4069 Cov.: 32

Gnomad AFR AF: 0.0531

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0532

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.195 AC: 29671 AN: 152142 Hom.: 4067 Cov.: 32 AF XY: 0.187 AC XY: 13926 AN XY: 74368

African (AFR) AF: 0.0530 AC: 2199 AN: 41524

American (AMR) AF: 0.141 AC: 2151 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 648 AN: 3470

East Asian (EAS) AF: 0.000964 AC: 5 AN: 5186

South Asian (SAS) AF: 0.0533 AC: 257 AN: 4824

European-Finnish (FIN) AF: 0.270 AC: 2845 AN: 10552

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 21033 AN: 67974

Other (OTH) AF: 0.188 AC: 396 AN: 2112

Alfa AF: 0.266 Hom.: 26805

Bravo AF: 0.182

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.4
DANN	Benign	0.78
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs2470893; hg19: chr15-75019449;