rs9558546

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;