rs9551180

Variant names:

• chr13-25143410-C-A
• rs9551180

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 0.157 in 152,100 control chromosomes in the GnomAD database, including 1,987 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 0.16 (1987 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.289 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: 0.157 AC: 23856 AN: 151984 Hom.: 1984 Cov.: 33

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.0956

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.157 AC: 23865 AN: 152100 Hom.: 1987 Cov.: 33 AF XY: 0.161 AC XY: 11999 AN XY: 74346

African (AFR) AF: 0.139 AC: 5764 AN: 41478

American (AMR) AF: 0.181 AC: 2771 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3468

East Asian (EAS) AF: 0.302 AC: 1559 AN: 5164

South Asian (SAS) AF: 0.263 AC: 1269 AN: 4818

European-Finnish (FIN) AF: 0.166 AC: 1758 AN: 10570

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9744 AN: 68006

Other (OTH) AF: 0.161 AC: 339 AN: 2106

Alfa AF: 0.152 Hom.: 2588

Bravo AF: 0.157

Asia WGS AF: 0.253 AC: 878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	12
DANN	Benign	0.66
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs9551180; hg19: chr13-25717548;