8-133626015-G-T

Variant names:

• chr8-133626015-G-T
• rs3958181

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 0.252 in 152,172 control chromosomes in the GnomAD database, including 5,338 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 0.25 (5338 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.954
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38281 AN: 152054 Hom.: 5340 Cov.: 33

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.0267

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.252 AC: 38297 AN: 152172 Hom.: 5338 Cov.: 33 AF XY: 0.249 AC XY: 18506 AN XY: 74394

African (AFR) AF: 0.344 AC: 14293 AN: 41490

American (AMR) AF: 0.221 AC: 3387 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1248 AN: 3468

East Asian (EAS) AF: 0.0266 AC: 138 AN: 5188

South Asian (SAS) AF: 0.261 AC: 1257 AN: 4810

European-Finnish (FIN) AF: 0.148 AC: 1563 AN: 10594

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15433 AN: 67998

Other (OTH) AF: 0.294 AC: 622 AN: 2114

Alfa AF: 0.242 Hom.: 14886

Bravo AF: 0.259

Asia WGS AF: 0.150 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.31
DANN	Benign	0.68
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs3958181; hg19: chr8-134638258;