2-233916448-T-C

Variant names:

• chr2-233916448-T-C
• rs10166942

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 0.399 in 152,076 control chromosomes in the GnomAD database, including 17,691 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 0.40 (17691 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 85 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.795 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: 0.399 AC: 60623 AN: 151958 Hom.: 17643 Cov.: 32

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.399 AC: 60736 AN: 152076 Hom.: 17691 Cov.: 32 AF XY: 0.399 AC XY: 29683 AN XY: 74342

African (AFR) AF: 0.803 AC: 33274 AN: 41456

American (AMR) AF: 0.355 AC: 5427 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 545 AN: 3466

East Asian (EAS) AF: 0.647 AC: 3333 AN: 5152

South Asian (SAS) AF: 0.441 AC: 2130 AN: 4828

European-Finnish (FIN) AF: 0.159 AC: 1685 AN: 10596

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13263 AN: 67970

Other (OTH) AF: 0.346 AC: 732 AN: 2114

Alfa AF: 0.260 Hom.: 24009

Bravo AF: 0.428

Asia WGS AF: 0.600 AC: 2086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.3
DANN	Benign	0.68
PhyloP100		-0.061

Splicing

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

Other links and lift over

dbSNP: rs10166942; hg19: chr2-234825093;