chr2-231933151-C-T

Variant names:

• chr2-231933151-C-T
• rs2679178

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 0.0735 in 152,096 control chromosomes in the GnomAD database, including 485 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 0.073 (485 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0903 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: 0.0735 AC: 11175 AN: 151978 Hom.: 485 Cov.: 31

Gnomad AFR AF: 0.0663

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.0595

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.00348

Gnomad SAS AF: 0.0963

Gnomad FIN AF: 0.0335

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0851

Gnomad OTH AF: 0.0872

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

GnomAD4 genome AF: 0.0735 AC: 11172 AN: 152096 Hom.: 485 Cov.: 31 AF XY: 0.0708 AC XY: 5268 AN XY: 74370

African (AFR) AF: 0.0661 AC: 2744 AN: 41496

American (AMR) AF: 0.0593 AC: 907 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 528 AN: 3470

East Asian (EAS) AF: 0.00349 AC: 18 AN: 5164

South Asian (SAS) AF: 0.0976 AC: 470 AN: 4816

European-Finnish (FIN) AF: 0.0335 AC: 355 AN: 10592

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.0851 AC: 5782 AN: 67960

Other (OTH) AF: 0.0859 AC: 181 AN: 2108

Alfa AF: 0.0841 Hom.: 440

Bravo AF: 0.0749

Asia WGS AF: 0.0380 AC: 133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.1
DANN	Benign	0.73
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs2679178; hg19: chr2-232797861;