2-118638115-T-C

Variant names:

• chr2-118638115-T-C
• rs651477

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 0.26 in 152,022 control chromosomes in the GnomAD database, including 5,365 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 0.26 (5365 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.385 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: 0.260 AC: 39563 AN: 151904 Hom.: 5356 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.260 AC: 39587 AN: 152022 Hom.: 5365 Cov.: 32 AF XY: 0.263 AC XY: 19552 AN XY: 74322

African (AFR) AF: 0.223 AC: 9229 AN: 41462

American (AMR) AF: 0.276 AC: 4212 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 1001 AN: 3470

East Asian (EAS) AF: 0.182 AC: 940 AN: 5160

South Asian (SAS) AF: 0.400 AC: 1928 AN: 4822

European-Finnish (FIN) AF: 0.292 AC: 3094 AN: 10578

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18311 AN: 67942

Other (OTH) AF: 0.263 AC: 555 AN: 2114

Alfa AF: 0.263 Hom.: 12246

Bravo AF: 0.254

Asia WGS AF: 0.282 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.53
DANN	Benign	0.80
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs651477; hg19: chr2-119395691;