rs2542061

Positions:

• chr11-116801515-A-G
• chr11-116801515-A-T

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 0.393 in 150,918 control chromosomes in the GnomAD database, including 13,795 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 0.39 (13795 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59351 AN: 150800 Hom.: 13800 Cov.: 31

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.393 AC: 59349 AN: 150918 Hom.: 13795 Cov.: 31 AF XY: 0.386 AC XY: 28503 AN XY: 73778

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.419

Alfa AF: 0.396 Hom.: 1979

Bravo AF: 0.384

Asia WGS AF: 0.347 AC: 1208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2542061; hg19: chr11-116672231;