chr8-139289510-C-T

Variant names:

• chr8-139289510-C-T
• rs4736239

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.682

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.609

Alfa AF: 0.681 Hom.: 71430

Bravo AF: 0.614

Asia WGS AF: 0.728 AC: 2533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4736239; hg19: chr8-140301753;