rs17463995

Variant names:

• chr15-48711575-T-C
• rs17463995

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 0.429 in 151,444 control chromosomes in the GnomAD database, including 15,017 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 (15017 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261
• Publications: 3 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 (SAS) allele frequency at 95% confidence interval = 0.505 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: 0.430 AC: 65037 AN: 151338 Hom.: 15016 Cov.: 30

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.429 AC: 65043 AN: 151444 Hom.: 15017 Cov.: 30 AF XY: 0.431 AC XY: 31839 AN XY: 73900

African (AFR) AF: 0.259 AC: 10703 AN: 41250

American (AMR) AF: 0.455 AC: 6930 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2057 AN: 3468

East Asian (EAS) AF: 0.254 AC: 1298 AN: 5108

South Asian (SAS) AF: 0.522 AC: 2500 AN: 4786

European-Finnish (FIN) AF: 0.531 AC: 5523 AN: 10396

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.507 AC: 34424 AN: 67906

Other (OTH) AF: 0.466 AC: 977 AN: 2098

Alfa AF: 0.486 Hom.: 51205

Bravo AF: 0.412

Asia WGS AF: 0.361 AC: 1252 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	1.8
DANN	Benign	0.66
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs17463995; hg19: chr15-49003772;