rs9533208

Variant names:

• chr13-42669655-T-A
• rs9533208

Your query was ambiguous. Multiple possible variants found:

• chr13-42669655-T-A
• chr13-42669655-T-C
• chr13-42669655-T-G

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 0.815 in 152,180 control chromosomes in the GnomAD database, including 51,535 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 0.81 (51535 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.898 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: 0.815 AC: 123906 AN: 152062 Hom.: 51521 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.946

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.832

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

GnomAD4 genome AF: 0.815 AC: 123956 AN: 152180 Hom.: 51535 Cov.: 32 AF XY: 0.815 AC XY: 60641 AN XY: 74404

African (AFR) AF: 0.643 AC: 26677 AN: 41482

American (AMR) AF: 0.761 AC: 11645 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.870 AC: 3019 AN: 3470

East Asian (EAS) AF: 0.757 AC: 3911 AN: 5166

South Asian (SAS) AF: 0.902 AC: 4353 AN: 4826

European-Finnish (FIN) AF: 0.946 AC: 10036 AN: 10612

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.904 AC: 61508 AN: 68004

Other (OTH) AF: 0.836 AC: 1768 AN: 2116

Alfa AF: 0.854 Hom.: 6979

Bravo AF: 0.789

Asia WGS AF: 0.818 AC: 2846 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
DANN	Benign	0.76
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs9533208; hg19: chr13-43243791;