2-118121677-C-T

Variant names:

• chr2-118121677-C-T
• rs1808458

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 0.0741 in 152,186 control chromosomes in the GnomAD database, including 525 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 0.074 (525 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.102 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: 0.0738 AC: 11226 AN: 152070 Hom.: 514 Cov.: 33

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0604

Gnomad ASJ AF: 0.0513

Gnomad EAS AF: 0.0210

Gnomad SAS AF: 0.0480

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0565

Gnomad OTH AF: 0.0592

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

GnomAD4 genome AF: 0.0741 AC: 11270 AN: 152186 Hom.: 525 Cov.: 33 AF XY: 0.0761 AC XY: 5663 AN XY: 74412

African (AFR) AF: 0.105 AC: 4351 AN: 41504

American (AMR) AF: 0.0605 AC: 925 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0513 AC: 178 AN: 3470

East Asian (EAS) AF: 0.0208 AC: 108 AN: 5180

South Asian (SAS) AF: 0.0481 AC: 232 AN: 4828

European-Finnish (FIN) AF: 0.128 AC: 1357 AN: 10572

Middle Eastern (MID) AF: 0.0308 AC: 9 AN: 292

European-Non Finnish (NFE) AF: 0.0565 AC: 3842 AN: 68016

Other (OTH) AF: 0.0662 AC: 140 AN: 2116

Alfa AF: 0.0614 Hom.: 718

Bravo AF: 0.0728

Asia WGS AF: 0.0610 AC: 211 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.62
PhyloP100		-0.015

Splicing

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

Other links and lift over

dbSNP: rs1808458; hg19: chr2-118879253; COSMIC: COSV60100177;