8-139483999-C-T

Variant names:

• chr8-139483999-C-T
• rs4645543

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 205 gene

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: 0.0452 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

African (AFR) AF: 0.0455 AC: 1891 AN: 41558

American (AMR) AF: 0.0179 AC: 274 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0873 AC: 303 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5190

South Asian (SAS) AF: 0.0367 AC: 177 AN: 4828

European-Finnish (FIN) AF: 0.0941 AC: 997 AN: 10600

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0462 AC: 3145 AN: 68024

Other (OTH) AF: 0.0364 AC: 77 AN: 2114

Alfa AF: 0.0467 Hom.: 58

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
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs4645543; hg19: chr8-140496242;