5-42387748-G-T

Variant names:

• chr5-42387748-G-T
• rs9686286

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 0.822 in 152,222 control chromosomes in the GnomAD database, including 51,705 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 0.82 (51705 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.822 AC: 125054 AN: 152104 Hom.: 51652 Cov.: 33

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.805

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

GnomAD4 genome AF: 0.822 AC: 125166 AN: 152222 Hom.: 51705 Cov.: 33 AF XY: 0.829 AC XY: 61720 AN XY: 74424

African (AFR) AF: 0.800 AC: 33190 AN: 41512

American (AMR) AF: 0.840 AC: 12843 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.771 AC: 2674 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5186 AN: 5192

South Asian (SAS) AF: 0.854 AC: 4122 AN: 4824

European-Finnish (FIN) AF: 0.922 AC: 9796 AN: 10620

Middle Eastern (MID) AF: 0.723 AC: 211 AN: 292

European-Non Finnish (NFE) AF: 0.805 AC: 54733 AN: 67994

Other (OTH) AF: 0.807 AC: 1703 AN: 2110

Alfa AF: 0.796 Hom.: 2823

Bravo AF: 0.814

Asia WGS AF: 0.931 AC: 3239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.71
DANN	Benign	0.40
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs9686286; hg19: chr5-42387850;