rs532040

Variant names:

• chr11-129706081-G-A
• rs532040

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 0.185 in 152,122 control chromosomes in the GnomAD database, including 2,933 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 0.19 (2933 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.227 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: 0.185 AC: 28154 AN: 152004 Hom.: 2931 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0233

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.185 AC: 28186 AN: 152122 Hom.: 2933 Cov.: 32 AF XY: 0.182 AC XY: 13553 AN XY: 74354

African (AFR) AF: 0.111 AC: 4604 AN: 41504

American (AMR) AF: 0.233 AC: 3561 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 669 AN: 3466

East Asian (EAS) AF: 0.0238 AC: 123 AN: 5176

South Asian (SAS) AF: 0.190 AC: 915 AN: 4816

European-Finnish (FIN) AF: 0.192 AC: 2025 AN: 10560

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15616 AN: 67994

Other (OTH) AF: 0.203 AC: 428 AN: 2110

Alfa AF: 0.220 Hom.: 3360

Bravo AF: 0.184

Asia WGS AF: 0.125 AC: 436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.055
DANN	Benign	0.52
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs532040; hg19: chr11-129575976;