rs13267998

Variant names:

• chr8-91405039-A-G
• rs13267998

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 0.0805 in 151,436 control chromosomes in the GnomAD database, including 633 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 0.080 (633 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.146 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: 0.0805 AC: 12174 AN: 151320 Hom.: 632 Cov.: 31

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0717

Gnomad ASJ AF: 0.0291

Gnomad EAS AF: 0.0312

Gnomad SAS AF: 0.0452

Gnomad FIN AF: 0.0184

Gnomad MID AF: 0.0287

Gnomad NFE AF: 0.0592

Gnomad OTH AF: 0.0864

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

GnomAD4 genome AF: 0.0805 AC: 12186 AN: 151436 Hom.: 633 Cov.: 31 AF XY: 0.0765 AC XY: 5657 AN XY: 73992

African (AFR) AF: 0.149 AC: 6162 AN: 41276

American (AMR) AF: 0.0716 AC: 1088 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.0291 AC: 101 AN: 3472

East Asian (EAS) AF: 0.0314 AC: 162 AN: 5152

South Asian (SAS) AF: 0.0455 AC: 218 AN: 4792

European-Finnish (FIN) AF: 0.0184 AC: 191 AN: 10396

Middle Eastern (MID) AF: 0.0205 AC: 6 AN: 292

European-Non Finnish (NFE) AF: 0.0592 AC: 4019 AN: 67838

Other (OTH) AF: 0.0851 AC: 179 AN: 2104

Alfa AF: 0.0659 Hom.: 614

Bravo AF: 0.0887

Asia WGS AF: 0.0500 AC: 173 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	3.7
DANN	Benign	0.41
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs13267998; hg19: chr8-92417267; COSMIC: COSV66722434;