8-5372618-C-T

Variant names:

• chr8-5372618-C-T
• rs9314565

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 0.536 in 151,874 control chromosomes in the GnomAD database, including 21,846 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 0.54 (21846 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 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: 0.536 AC: 81349 AN: 151756 Hom.: 21827 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.536 AC: 81412 AN: 151874 Hom.: 21846 Cov.: 32 AF XY: 0.536 AC XY: 39800 AN XY: 74202

African (AFR) AF: 0.504 AC: 20884 AN: 41402

American (AMR) AF: 0.545 AC: 8316 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1997 AN: 3470

East Asian (EAS) AF: 0.399 AC: 2062 AN: 5170

South Asian (SAS) AF: 0.535 AC: 2579 AN: 4820

European-Finnish (FIN) AF: 0.541 AC: 5684 AN: 10514

Middle Eastern (MID) AF: 0.671 AC: 196 AN: 292

European-Non Finnish (NFE) AF: 0.560 AC: 38033 AN: 67948

Other (OTH) AF: 0.558 AC: 1175 AN: 2106

Alfa AF: 0.556 Hom.: 92254

Bravo AF: 0.535

Asia WGS AF: 0.480 AC: 1668 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.28
DANN	Benign	0.34
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs9314565; hg19: chr8-5230140;