rs6598500

Variant names:

• chr15-101841157-C-T
• rs6598500

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 0.533 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.735 AC: 30409 AN: 41366

American (AMR) AF: 0.454 AC: 6910 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1568 AN: 3468

East Asian (EAS) AF: 0.176 AC: 904 AN: 5144

South Asian (SAS) AF: 0.434 AC: 2077 AN: 4790

European-Finnish (FIN) AF: 0.349 AC: 3677 AN: 10524

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33683 AN: 67918

Other (OTH) AF: 0.502 AC: 1062 AN: 2114

Alfa AF: 0.497 Hom.: 28658

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
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs6598500; hg19: chr15-102381360;