rs2470893

Positions:

• chr15-74727108-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0530

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.0533

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.188

Alfa AF: 0.276 Hom.: 13053

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2470893; hg19: chr15-75019449;