chr2-5450125-T-C

Variant names:

• chr2-5450125-T-C
• rs813779

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.385

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.728

Gnomad4 EAS AF: 0.972

Gnomad4 SAS AF: 0.891

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.798

Gnomad4 OTH AF: 0.703

Alfa AF: 0.779 Hom.: 58635

Bravo AF: 0.671

Asia WGS AF: 0.893 AC: 3106 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs813779; hg19: chr2-5590257;