rs11582540

Variant names:

• chr1-47544325-C-A
• rs11582540

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 0.156 in 152,034 control chromosomes in the GnomAD database, including 2,391 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 (2391 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23711 AN: 151916 Hom.: 2381 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.0844

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0945

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.156 AC: 23751 AN: 152034 Hom.: 2391 Cov.: 32 AF XY: 0.157 AC XY: 11695 AN XY: 74316

African (AFR) AF: 0.286 AC: 11865 AN: 41422

American (AMR) AF: 0.135 AC: 2071 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0844 AC: 293 AN: 3472

East Asian (EAS) AF: 0.157 AC: 806 AN: 5146

South Asian (SAS) AF: 0.109 AC: 526 AN: 4818

European-Finnish (FIN) AF: 0.123 AC: 1298 AN: 10562

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0945 AC: 6429 AN: 68004

Other (OTH) AF: 0.158 AC: 333 AN: 2112

Alfa AF: 0.0752 Hom.: 182

Bravo AF: 0.162

Asia WGS AF: 0.138 AC: 480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.79
DANN	Benign	0.75
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs11582540; hg19: chr1-48009997;