chr5-24913058-G-T

Variant names:

• chr5-24913058-G-T
• rs9283778

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 0.714 in 151,770 control chromosomes in the GnomAD database, including 39,397 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 0.71 (39397 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.821 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: 0.714 AC: 108312 AN: 151652 Hom.: 39384 Cov.: 33

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.842

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.714 AC: 108360 AN: 151770 Hom.: 39397 Cov.: 33 AF XY: 0.717 AC XY: 53193 AN XY: 74146

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.739

Gnomad4 EAS AF: 0.742

Gnomad4 SAS AF: 0.843

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.772

Gnomad4 OTH AF: 0.719

Alfa AF: 0.764 Hom.: 64832

Bravo AF: 0.713

Asia WGS AF: 0.725 AC: 2508 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9283778; hg19: chr5-24913167;