2-187629345-C-T

Variant names:

• chr2-187629345-C-T
• rs2176858

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 0.1 in 151,984 control chromosomes in the GnomAD database, including 1,127 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 0.10 (1127 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.195 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: 0.100 AC: 15187 AN: 151866 Hom.: 1124 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.0174

Gnomad SAS AF: 0.0504

Gnomad FIN AF: 0.0262

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0576

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.100 AC: 15223 AN: 151984 Hom.: 1127 Cov.: 32 AF XY: 0.0985 AC XY: 7315 AN XY: 74280

African (AFR) AF: 0.199 AC: 8217 AN: 41386

American (AMR) AF: 0.130 AC: 1985 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0709 AC: 246 AN: 3468

East Asian (EAS) AF: 0.0174 AC: 90 AN: 5168

South Asian (SAS) AF: 0.0502 AC: 242 AN: 4820

European-Finnish (FIN) AF: 0.0262 AC: 277 AN: 10578

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0576 AC: 3917 AN: 67978

Other (OTH) AF: 0.0993 AC: 210 AN: 2114

Alfa AF: 0.0629 Hom.: 260

Bravo AF: 0.113

Asia WGS AF: 0.0570 AC: 201 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	2.6
DANN	Benign	0.16
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs2176858; hg19: chr2-188494072;