2-233905414-C-T

Variant names:

• chr2-233905414-C-T
• rs10187654

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 0.397 in 152,014 control chromosomes in the GnomAD database, including 17,548 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 (17548 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.657
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 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: 0.396 AC: 60188 AN: 151896 Hom.: 17499 Cov.: 31

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.397 AC: 60302 AN: 152014 Hom.: 17548 Cov.: 31 AF XY: 0.397 AC XY: 29496 AN XY: 74300

African (AFR) AF: 0.801 AC: 33226 AN: 41488

American (AMR) AF: 0.355 AC: 5416 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 550 AN: 3466

East Asian (EAS) AF: 0.642 AC: 3307 AN: 5150

South Asian (SAS) AF: 0.440 AC: 2111 AN: 4800

European-Finnish (FIN) AF: 0.158 AC: 1675 AN: 10576

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.190 AC: 12942 AN: 67948

Other (OTH) AF: 0.346 AC: 730 AN: 2110

Alfa AF: 0.277 Hom.: 16480

Bravo AF: 0.425

Asia WGS AF: 0.600 AC: 2085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.069
DANN	Benign	0.36
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs10187654; hg19: chr2-234814059;