chr2-234394166-C-T

Variant names:

• chr2-234394166-C-T
• rs11887188

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 0.108 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0963

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.0965

Gnomad4 EAS AF: 0.0193

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.115

Alfa AF: 0.107 Hom.: 198

Bravo AF: 0.107

Asia WGS AF: 0.0880 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11887188; hg19: chr2-235302810;