rs2542052

Variant names:

• chr11-116829268-A-C
• rs2542052

Your query was ambiguous. Multiple possible variants found:

• chr11-116829268-A-C
• chr11-116829268-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.66 (21236 hom., cov: 19)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.697 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: 0.657 AC: 77042 AN: 117188 Hom.: 21243 Cov.: 19

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.657 AC: 77063 AN: 117254 Hom.: 21236 Cov.: 19 AF XY: 0.652 AC XY: 37081 AN XY: 56912

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.702

Gnomad4 OTH AF: 0.654

Alfa AF: 0.600 Hom.: 24419

Bravo AF: 0.520

Asia WGS AF: 0.490 AC: 1698 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.5
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2542052; hg19: chr11-116699984;