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. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.277 AC: 11496 AN: 41464

American (AMR) AF: 0.418 AC: 6380 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 745 AN: 3470

East Asian (EAS) AF: 0.637 AC: 3284 AN: 5152

South Asian (SAS) AF: 0.241 AC: 1162 AN: 4816

European-Finnish (FIN) AF: 0.338 AC: 3581 AN: 10586

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17422 AN: 67984

Other (OTH) AF: 0.284 AC: 601 AN: 2114

Alfa AF: 0.277 Hom.: 15839

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
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs9558546; hg19: chr13-106061902;