2-234394166-C-T

Variant names:

• chr2-234394166-C-T
• rs11887188

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 0.108 in 152,250 control chromosomes in the GnomAD database, including 936 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 0.11 (936 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16359 AN: 152132 Hom.: 933 Cov.: 33

Gnomad AFR AF: 0.0963

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0965

Gnomad EAS AF: 0.0192

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.108 AC: 16377 AN: 152250 Hom.: 936 Cov.: 33 AF XY: 0.106 AC XY: 7910 AN XY: 74438

African (AFR) AF: 0.0963 AC: 4002 AN: 41538

American (AMR) AF: 0.114 AC: 1737 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0965 AC: 335 AN: 3470

East Asian (EAS) AF: 0.0193 AC: 100 AN: 5186

South Asian (SAS) AF: 0.194 AC: 932 AN: 4816

European-Finnish (FIN) AF: 0.107 AC: 1136 AN: 10610

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7723 AN: 68004

Other (OTH) AF: 0.115 AC: 244 AN: 2116

Alfa AF: 0.107 Hom.: 1549

Bravo AF: 0.107

Asia WGS AF: 0.0880 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.31
DANN	Benign	0.51
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs11887188; hg19: chr2-235302810;