5-24913058-G-T

Variant names:

• chr5-24913058-G-T
• rs9283778

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 0.714 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
• Publications: 3 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 (SAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.562 AC: 23255 AN: 41384

American (AMR) AF: 0.801 AC: 12202 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.739 AC: 2559 AN: 3464

East Asian (EAS) AF: 0.742 AC: 3835 AN: 5170

South Asian (SAS) AF: 0.843 AC: 4062 AN: 4820

European-Finnish (FIN) AF: 0.718 AC: 7566 AN: 10544

Middle Eastern (MID) AF: 0.788 AC: 230 AN: 292

European-Non Finnish (NFE) AF: 0.772 AC: 52409 AN: 67850

Other (OTH) AF: 0.719 AC: 1515 AN: 2106

Alfa AF: 0.757 Hom.: 141306

Bravo AF: 0.713

Asia WGS AF: 0.725 AC: 2508 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.59
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs9283778; hg19: chr5-24913167;