rs6598500

Variant names:

• chr15-101841157-C-T
• rs6598500

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;