rs11590090

Variant names:

• chr1-112770941-C-A
• rs11590090

Your query was ambiguous. Multiple possible variants found:

• chr1-112770941-C-A
• chr1-112770941-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 0.244 in 151,986 control chromosomes in the GnomAD database, including 4,873 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 0.24 (4873 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.87
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.302 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: 0.245 AC: 37135 AN: 151868 Hom.: 4871 Cov.: 31

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.244 AC: 37138 AN: 151986 Hom.: 4873 Cov.: 31 AF XY: 0.238 AC XY: 17699 AN XY: 74278

African (AFR) AF: 0.173 AC: 7173 AN: 41472

American (AMR) AF: 0.189 AC: 2884 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 764 AN: 3468

East Asian (EAS) AF: 0.132 AC: 682 AN: 5176

South Asian (SAS) AF: 0.248 AC: 1190 AN: 4806

European-Finnish (FIN) AF: 0.264 AC: 2783 AN: 10540

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20782 AN: 67954

Other (OTH) AF: 0.237 AC: 499 AN: 2104

Alfa AF: 0.281 Hom.: 16718

Bravo AF: 0.234

Asia WGS AF: 0.185 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0070
DANN	Benign	0.43
PhyloP100		-4.9

Splicing

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

Other links and lift over

dbSNP: rs11590090; hg19: chr1-113313563;