8-5189308-C-T

Variant names:

• chr8-5189308-C-T
• rs6983297

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 0.463 in 151,920 control chromosomes in the GnomAD database, including 16,635 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 0.46 (16635 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.575 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: 0.463 AC: 70231 AN: 151802 Hom.: 16613 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.463 AC: 70296 AN: 151920 Hom.: 16635 Cov.: 32 AF XY: 0.458 AC XY: 34001 AN XY: 74252

African (AFR) AF: 0.581 AC: 24055 AN: 41408

American (AMR) AF: 0.404 AC: 6177 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1842 AN: 3470

East Asian (EAS) AF: 0.402 AC: 2077 AN: 5166

South Asian (SAS) AF: 0.469 AC: 2253 AN: 4806

European-Finnish (FIN) AF: 0.388 AC: 4093 AN: 10544

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28156 AN: 67938

Other (OTH) AF: 0.468 AC: 990 AN: 2114

Alfa AF: 0.262 Hom.: 552

Bravo AF: 0.469

Asia WGS AF: 0.411 AC: 1432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.5
DANN	Benign	0.65
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs6983297; hg19: chr8-5046830;