chr2-232404005-C-T

Variant names:

• chr2-232404005-C-T
• rs2697766

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 0.38 in 151,772 control chromosomes in the GnomAD database, including 11,245 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 0.38 (11245 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 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: 0.380 AC: 57556 AN: 151654 Hom.: 11224 Cov.: 31

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.506

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.380 AC: 57605 AN: 151772 Hom.: 11245 Cov.: 31 AF XY: 0.374 AC XY: 27706 AN XY: 74154

African (AFR) AF: 0.459 AC: 18998 AN: 41374

American (AMR) AF: 0.289 AC: 4408 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1302 AN: 3472

East Asian (EAS) AF: 0.338 AC: 1744 AN: 5162

South Asian (SAS) AF: 0.282 AC: 1346 AN: 4766

European-Finnish (FIN) AF: 0.312 AC: 3273 AN: 10506

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.370 AC: 25160 AN: 67912

Other (OTH) AF: 0.381 AC: 806 AN: 2114

Alfa AF: 0.368 Hom.: 22437

Bravo AF: 0.382

Asia WGS AF: 0.288 AC: 1005 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.17
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs2697766; hg19: chr2-233268715;