rs2011946

Positions:

• chr2-136060046-C-A

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.136060046C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;