rs9558546

Variant names:

• chr13-105409553-A-G
• rs9558546

Your query was ambiguous. Multiple possible variants found:

• chr13-105409553-A-G
• chr13-105409553-A-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 0.296 in 152,070 control chromosomes in the GnomAD database, including 7,175 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 0.30 (7175 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.561

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.619 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: 0.296 AC: 44913 AN: 151952 Hom.: 7160 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.296 AC: 44948 AN: 152070 Hom.: 7175 Cov.: 32 AF XY: 0.301 AC XY: 22356 AN XY: 74340

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.284

Alfa AF: 0.271 Hom.: 5575

Bravo AF: 0.306

Asia WGS AF: 0.402 AC: 1395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9558546; hg19: chr13-106061902;