rs2011946

Variant names:

• chr2-136060046-C-A
• rs2011946

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 0.451 in 152,146 control chromosomes in the GnomAD database, including 19,655 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 0.45 (19655 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103

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 = 0.651 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: 0.451 AC: 68582 AN: 152028 Hom.: 19649 Cov.: 34

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.451 AC: 68611 AN: 152146 Hom.: 19655 Cov.: 34 AF XY: 0.441 AC XY: 32772 AN XY: 74392

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.656

Gnomad4 OTH AF: 0.379

Alfa AF: 0.562 Hom.: 16896

Bravo AF: 0.418

Asia WGS AF: 0.166 AC: 580 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	2.0
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2011946; hg19: chr2-136817616;