chr2-231933256-C-T

Variant names:

• chr2-231933256-C-T
• rs2580816

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.279 in 151,174 control chromosomes in the GnomAD database, including 6,787 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 0.28 (6787 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149
• Publications: 36 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42177 AN: 151056 Hom.: 6770 Cov.: 29

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.298

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.279 AC: 42233 AN: 151174 Hom.: 6787 Cov.: 29 AF XY: 0.281 AC XY: 20727 AN XY: 73782

African (AFR) AF: 0.369 AC: 15189 AN: 41132

American (AMR) AF: 0.391 AC: 5932 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 976 AN: 3462

East Asian (EAS) AF: 0.549 AC: 2762 AN: 5032

South Asian (SAS) AF: 0.317 AC: 1514 AN: 4778

European-Finnish (FIN) AF: 0.146 AC: 1523 AN: 10456

Middle Eastern (MID) AF: 0.303 AC: 88 AN: 290

European-Non Finnish (NFE) AF: 0.197 AC: 13371 AN: 67836

Other (OTH) AF: 0.292 AC: 614 AN: 2102

Alfa AF: 0.234 Hom.: 22056

Bravo AF: 0.307

Asia WGS AF: 0.378 AC: 1316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	13
DANN	Benign	0.81
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs2580816; hg19: chr2-232797966;