8-139289510-C-T

Variant names:

• chr8-139289510-C-T
• rs4736239

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 0.626 in 152,106 control chromosomes in the GnomAD database, including 30,708 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 0.63 (30708 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.03
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.743 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: 0.626 AC: 95215 AN: 151988 Hom.: 30690 Cov.: 33

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.626 AC: 95273 AN: 152106 Hom.: 30708 Cov.: 33 AF XY: 0.632 AC XY: 46962 AN XY: 74342

African (AFR) AF: 0.460 AC: 19064 AN: 41478

American (AMR) AF: 0.659 AC: 10077 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2179 AN: 3470

East Asian (EAS) AF: 0.682 AC: 3528 AN: 5176

South Asian (SAS) AF: 0.764 AC: 3672 AN: 4806

European-Finnish (FIN) AF: 0.706 AC: 7477 AN: 10586

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47187 AN: 67984

Other (OTH) AF: 0.609 AC: 1284 AN: 2108

Alfa AF: 0.674 Hom.: 145794

Bravo AF: 0.614

Asia WGS AF: 0.728 AC: 2533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0060
DANN	Benign	0.60
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs4736239; hg19: chr8-140301753;