chr8-139483999-C-T

Position:

• chr8-139483999-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0452 in 152,286 control chromosomes in the GnomAD database, including 205 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 0.045 (205 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0452 (6878/152286) while in subpopulation NFE AF= 0.0462 (3145/68024). AF 95% confidence interval is 0.0449. There are 205 homozygotes in gnomad4. There are 3478 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 205 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0452 AC: 6873 AN: 152168 Hom.: 204 Cov.: 33

Gnomad AFR AF: 0.0455

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0179

Gnomad ASJ AF: 0.0873

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0370

Gnomad FIN AF: 0.0941

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0462

Gnomad OTH AF: 0.0368

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

GnomAD4 genome AF: 0.0452 AC: 6878 AN: 152286 Hom.: 205 Cov.: 33 AF XY: 0.0467 AC XY: 3478 AN XY: 74452

Gnomad4 AFR AF: 0.0455

Gnomad4 AMR AF: 0.0179

Gnomad4 ASJ AF: 0.0873

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0367

Gnomad4 FIN AF: 0.0941

Gnomad4 NFE AF: 0.0462

Gnomad4 OTH AF: 0.0364

Alfa AF: 0.0481 Hom.: 35

Bravo AF: 0.0396

Asia WGS AF: 0.0230 AC: 81 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4645543; hg19: chr8-140496242;