rs532040

chr11-129706081-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.0238

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.203

Alfa AF: 0.220 Hom.: 2434

Bravo AF: 0.184

Asia WGS AF: 0.125 AC: 436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.055
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs532040; hg19: chr11-129575976;