chr2-5450125-T-C

Variant names:

• chr2-5450125-T-C
• rs813779

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 0.69 in 151,872 control chromosomes in the GnomAD database, including 38,987 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 0.69 (38987 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104769 AN: 151762 Hom.: 38987 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.690 AC: 104786 AN: 151872 Hom.: 38987 Cov.: 32 AF XY: 0.695 AC XY: 51593 AN XY: 74228

African (AFR) AF: 0.385 AC: 15933 AN: 41418

American (AMR) AF: 0.778 AC: 11878 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2524 AN: 3468

East Asian (EAS) AF: 0.972 AC: 5017 AN: 5164

South Asian (SAS) AF: 0.891 AC: 4295 AN: 4820

European-Finnish (FIN) AF: 0.816 AC: 8558 AN: 10492

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.798 AC: 54189 AN: 67948

Other (OTH) AF: 0.703 AC: 1480 AN: 2104

Alfa AF: 0.757 Hom.: 127226

Bravo AF: 0.671

Asia WGS AF: 0.893 AC: 3106 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.35
DANN	Benign	0.43
PhyloP100		-0.031

Splicing

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

Other links and lift over

dbSNP: rs813779; hg19: chr2-5590257;