rs9563238

Variant names:

• chr13-54563572-G-A
• rs9563238

Your query was ambiguous. Multiple possible variants found:

• chr13-54563572-G-A
• chr13-54563572-G-T

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 0.811 in 152,200 control chromosomes in the GnomAD database, including 50,134 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 (50134 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452
• Publications: 0 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 (AFR) allele frequency at 95% confidence interval = 0.845 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: 0.811 AC: 123397 AN: 152082 Hom.: 50085 Cov.: 33

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.811 AC: 123504 AN: 152200 Hom.: 50134 Cov.: 33 AF XY: 0.807 AC XY: 60019 AN XY: 74400

African (AFR) AF: 0.853 AC: 35444 AN: 41556

American (AMR) AF: 0.778 AC: 11897 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.828 AC: 2876 AN: 3472

East Asian (EAS) AF: 0.721 AC: 3722 AN: 5160

South Asian (SAS) AF: 0.831 AC: 4008 AN: 4826

European-Finnish (FIN) AF: 0.731 AC: 7734 AN: 10578

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.810 AC: 55101 AN: 68012

Other (OTH) AF: 0.810 AC: 1705 AN: 2106

Alfa AF: 0.812 Hom.: 36163

Bravo AF: 0.815

Asia WGS AF: 0.808 AC: 2811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.55
DANN	Benign	0.61
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs9563238; hg19: chr13-55137707;