rs1532096

Variant names:

• chr11-42891803-A-G
• rs1532096

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 0.121 in 151,992 control chromosomes in the GnomAD database, including 1,177 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 0.12 (1177 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170
• 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 (NFE) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18466 AN: 151874 Hom.: 1177 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.121 AC: 18466 AN: 151992 Hom.: 1177 Cov.: 32 AF XY: 0.122 AC XY: 9040 AN XY: 74320

African (AFR) AF: 0.106 AC: 4379 AN: 41370

American (AMR) AF: 0.108 AC: 1646 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 362 AN: 3466

East Asian (EAS) AF: 0.0110 AC: 57 AN: 5186

South Asian (SAS) AF: 0.103 AC: 496 AN: 4812

European-Finnish (FIN) AF: 0.149 AC: 1581 AN: 10592

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9547 AN: 67980

Other (OTH) AF: 0.124 AC: 262 AN: 2108

Alfa AF: 0.136 Hom.: 2354

Bravo AF: 0.117

Asia WGS AF: 0.0530 AC: 186 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.78
PhyloP100		0.017

Splicing

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

Other links and lift over

dbSNP: rs1532096; hg19: chr11-42913353;