rs725463

Variant names:

• chr15-59850880-C-T
• rs725463

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 0.491 in 151,942 control chromosomes in the GnomAD database, including 18,977 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 0.49 (18977 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 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: 0.491 AC: 74524 AN: 151822 Hom.: 18959 Cov.: 31

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.491 AC: 74580 AN: 151942 Hom.: 18977 Cov.: 31 AF XY: 0.484 AC XY: 35978 AN XY: 74280

Gnomad4 AFR AF: 0.592

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.457

Alfa AF: 0.475 Hom.: 28965

Bravo AF: 0.481

Asia WGS AF: 0.313 AC: 1090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.5
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs725463; hg19: chr15-60143079;