2-113134564-T-C

Variant names:

• chr2-113134564-T-C
• rs397211

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.273 in 151,942 control chromosomes in the GnomAD database, including 6,353 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 0.27 (6353 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.720
• Publications: 28 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41376 AN: 151824 Hom.: 6341 Cov.: 31

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.273 AC: 41405 AN: 151942 Hom.: 6353 Cov.: 31 AF XY: 0.277 AC XY: 20558 AN XY: 74238

African (AFR) AF: 0.140 AC: 5801 AN: 41442

American (AMR) AF: 0.436 AC: 6661 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1143 AN: 3464

East Asian (EAS) AF: 0.315 AC: 1626 AN: 5162

South Asian (SAS) AF: 0.374 AC: 1800 AN: 4812

European-Finnish (FIN) AF: 0.284 AC: 2990 AN: 10510

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20475 AN: 67956

Other (OTH) AF: 0.304 AC: 642 AN: 2110

Alfa AF: 0.280 Hom.: 3495

Bravo AF: 0.276

Asia WGS AF: 0.345 AC: 1200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.86
DANN	Benign	0.56
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs397211; hg19: chr2-113892141;