rs8000506

Variant names:

• chr13-100016739-C-G
• rs8000506

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 0.36 in 152,076 control chromosomes in the GnomAD database, including 10,482 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 0.36 (10482 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.433 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: 0.360 AC: 54771 AN: 151958 Hom.: 10481 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.360 AC: 54798 AN: 152076 Hom.: 10482 Cov.: 32 AF XY: 0.355 AC XY: 26399 AN XY: 74360

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.401

Alfa AF: 0.395 Hom.: 1532

Bravo AF: 0.358

Asia WGS AF: 0.224 AC: 785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.7
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8000506; hg19: chr13-100668993;