15-59850880-C-T

Variant names:

• chr15-59850880-C-T
• rs725463

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 0.491 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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.592 AC: 24523 AN: 41456

American (AMR) AF: 0.355 AC: 5419 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1478 AN: 3462

East Asian (EAS) AF: 0.218 AC: 1128 AN: 5164

South Asian (SAS) AF: 0.336 AC: 1615 AN: 4810

European-Finnish (FIN) AF: 0.509 AC: 5362 AN: 10530

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33561 AN: 67948

Other (OTH) AF: 0.457 AC: 960 AN: 2102

Alfa AF: 0.480 Hom.: 48130

Bravo AF: 0.481

Asia WGS AF: 0.313 AC: 1090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.5
DANN	Benign	0.67
PhyloP100		-0.033

Splicing

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

Other links and lift over

dbSNP: rs725463; hg19: chr15-60143079;