rs9555810

Variant names:

• chr13-111529090-C-G
• rs9555810

Your query was ambiguous. Multiple possible variants found:

• chr13-111529090-C-G
• chr13-111529090-C-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 0.256 in 152,104 control chromosomes in the GnomAD database, including 5,122 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 0.26 (5122 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.257 AC: 38989 AN: 151986 Hom.: 5124 Cov.: 33

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.256 AC: 38997 AN: 152104 Hom.: 5122 Cov.: 33 AF XY: 0.258 AC XY: 19198 AN XY: 74364

African (AFR) AF: 0.193 AC: 8024 AN: 41490

American (AMR) AF: 0.293 AC: 4471 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1072 AN: 3472

East Asian (EAS) AF: 0.168 AC: 872 AN: 5178

South Asian (SAS) AF: 0.282 AC: 1361 AN: 4820

European-Finnish (FIN) AF: 0.270 AC: 2853 AN: 10558

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19338 AN: 67996

Other (OTH) AF: 0.292 AC: 618 AN: 2116

Alfa AF: 0.258 Hom.: 2979

Bravo AF: 0.254

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.9
DANN	Benign	0.39
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs9555810; hg19: chr13-112181437;