rs6598500

chr15-101841157-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 0.533 in 151,740 control chromosomes in the GnomAD database, including 23,043 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 0.53 (23043 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 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: 0.533 AC: 80783 AN: 151622 Hom.: 23013 Cov.: 30

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.533 AC: 80866 AN: 151740 Hom.: 23043 Cov.: 30 AF XY: 0.522 AC XY: 38682 AN XY: 74118

Gnomad4 AFR AF: 0.735

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.502

Alfa AF: 0.495 Hom.: 23715

Bravo AF: 0.542

Asia WGS AF: 0.369 AC: 1282 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.0
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6598500; hg19: chr15-102381360;