2-232436106-T-C

Variant names:

• chr2-232436106-T-C
• rs12996863

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 0.213 in 152,202 control chromosomes in the GnomAD database, including 4,294 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 0.21 (4294 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921
• Publications: 6 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 (NFE) allele frequency at 95% confidence interval = 0.291 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: 0.213 AC: 32418 AN: 152084 Hom.: 4292 Cov.: 33

Gnomad AFR AF: 0.0678

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.213 AC: 32410 AN: 152202 Hom.: 4294 Cov.: 33 AF XY: 0.211 AC XY: 15701 AN XY: 74398

African (AFR) AF: 0.0676 AC: 2811 AN: 41556

American (AMR) AF: 0.203 AC: 3107 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1241 AN: 3470

East Asian (EAS) AF: 0.101 AC: 521 AN: 5174

South Asian (SAS) AF: 0.197 AC: 951 AN: 4816

European-Finnish (FIN) AF: 0.261 AC: 2760 AN: 10588

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20047 AN: 68002

Other (OTH) AF: 0.232 AC: 488 AN: 2104

Alfa AF: 0.261 Hom.: 16505

Bravo AF: 0.204

Asia WGS AF: 0.147 AC: 515 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	1.1
DANN	Benign	0.38
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs12996863; hg19: chr2-233300816;