rs5000507

Variant names:

• chr13-81514819-A-T
• rs5000507

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 0.405 in 152,000 control chromosomes in the GnomAD database, including 16,524 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 0.41 (16524 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.761 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: 0.405 AC: 61527 AN: 151882 Hom.: 16493 Cov.: 32

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.405 AC: 61611 AN: 152000 Hom.: 16524 Cov.: 32 AF XY: 0.394 AC XY: 29258 AN XY: 74314

African (AFR) AF: 0.768 AC: 31837 AN: 41464

American (AMR) AF: 0.263 AC: 4019 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 811 AN: 3464

East Asian (EAS) AF: 0.183 AC: 944 AN: 5148

South Asian (SAS) AF: 0.245 AC: 1180 AN: 4824

European-Finnish (FIN) AF: 0.198 AC: 2099 AN: 10580

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19588 AN: 67938

Other (OTH) AF: 0.373 AC: 786 AN: 2108

Alfa AF: 0.345 Hom.: 1516

Bravo AF: 0.425

Asia WGS AF: 0.259 AC: 901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	7.7
DANN	Benign	0.29
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs5000507; hg19: chr13-82088954;