rs11234542

Variant names:

• chr11-86092196-A-G
• rs11234542

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 0.17 in 151,944 control chromosomes in the GnomAD database, including 2,369 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 0.17 (2369 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 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: 0.169 AC: 25722 AN: 151826 Hom.: 2367 Cov.: 31

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.0980

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.170 AC: 25755 AN: 151944 Hom.: 2369 Cov.: 31 AF XY: 0.169 AC XY: 12533 AN XY: 74268

African (AFR) AF: 0.147 AC: 6090 AN: 41446

American (AMR) AF: 0.176 AC: 2689 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0980 AC: 340 AN: 3470

East Asian (EAS) AF: 0.375 AC: 1922 AN: 5120

South Asian (SAS) AF: 0.201 AC: 966 AN: 4802

European-Finnish (FIN) AF: 0.152 AC: 1607 AN: 10574

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11743 AN: 67974

Other (OTH) AF: 0.147 AC: 309 AN: 2108

Alfa AF: 0.167 Hom.: 2948

Bravo AF: 0.170

Asia WGS AF: 0.295 AC: 1023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.72
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs11234542; hg19: chr11-85803238;