rs13276600

Variant names:

• chr8-18413680-C-T
• rs13276600

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 0.388 in 151,848 control chromosomes in the GnomAD database, including 12,060 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 0.39 (12060 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.441 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: 0.388 AC: 58828 AN: 151730 Hom.: 12051 Cov.: 31

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.0888

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.388 AC: 58879 AN: 151848 Hom.: 12060 Cov.: 31 AF XY: 0.385 AC XY: 28551 AN XY: 74186

African (AFR) AF: 0.322 AC: 13310 AN: 41394

American (AMR) AF: 0.355 AC: 5414 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1574 AN: 3464

East Asian (EAS) AF: 0.0888 AC: 459 AN: 5170

South Asian (SAS) AF: 0.346 AC: 1666 AN: 4810

European-Finnish (FIN) AF: 0.468 AC: 4918 AN: 10516

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30243 AN: 67922

Other (OTH) AF: 0.395 AC: 831 AN: 2102

Alfa AF: 0.432 Hom.: 7624

Bravo AF: 0.376

Asia WGS AF: 0.221 AC: 770 AN: 3478

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	0.68
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs13276600; hg19: chr8-18271190;