rs17463995

Positions:

• chr15-48711575-T-C

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 0.429 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.531

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.466

Alfa AF: 0.498 Hom.: 38954

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17463995; hg19: chr15-49003772;