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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.853

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.828

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.831

Gnomad4 FIN AF: 0.731

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.810

Alfa AF: 0.811 Hom.: 26608

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9563238; hg19: chr13-55137707;