chr5-133843389-C-T

Variant names:

• chr5-133843389-C-T
• rs2457174

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 0.328 in 152,002 control chromosomes in the GnomAD database, including 9,125 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 0.33 (9125 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.425 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: 0.328 AC: 49779 AN: 151884 Hom.: 9125 Cov.: 31

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.0427

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.328 AC: 49785 AN: 152002 Hom.: 9125 Cov.: 31 AF XY: 0.318 AC XY: 23593 AN XY: 74288

African (AFR) AF: 0.215 AC: 8916 AN: 41444

American (AMR) AF: 0.301 AC: 4592 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1433 AN: 3468

East Asian (EAS) AF: 0.0426 AC: 221 AN: 5188

South Asian (SAS) AF: 0.187 AC: 901 AN: 4810

European-Finnish (FIN) AF: 0.318 AC: 3353 AN: 10552

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29143 AN: 67952

Other (OTH) AF: 0.333 AC: 701 AN: 2108

Alfa AF: 0.380 Hom.: 29317

Bravo AF: 0.319

Asia WGS AF: 0.120 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.6
DANN	Benign	0.75
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2457174; hg19: chr5-133179080;