rs2542051

Variant names:

• chr11-116827022-C-A
• rs2542051

Your query was ambiguous. Multiple possible variants found:

• chr11-116827022-C-A
• chr11-116827022-C-G

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 0.526 in 152,142 control chromosomes in the GnomAD database, including 22,499 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 0.53 (22499 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.624 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: 0.527 AC: 80076 AN: 152024 Hom.: 22501 Cov.: 33

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.526 AC: 80096 AN: 152142 Hom.: 22499 Cov.: 33 AF XY: 0.521 AC XY: 38788 AN XY: 74384

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.613

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.548

Alfa AF: 0.577 Hom.: 4504

Bravo AF: 0.525

Asia WGS AF: 0.536 AC: 1867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.022
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2542051; hg19: chr11-116697738;