rs725463

chr15-59850880-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 0.491 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;