8-104266574-T-G

Variant names:

• chr8-104266574-T-G
• rs4734754

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 0.404 in 152,076 control chromosomes in the GnomAD database, including 12,917 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 0.40 (12917 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.63
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 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: 0.404 AC: 61446 AN: 151958 Hom.: 12902 Cov.: 33

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.404 AC: 61505 AN: 152076 Hom.: 12917 Cov.: 33 AF XY: 0.409 AC XY: 30425 AN XY: 74340

African (AFR) AF: 0.461 AC: 19097 AN: 41450

American (AMR) AF: 0.482 AC: 7365 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1271 AN: 3470

East Asian (EAS) AF: 0.631 AC: 3264 AN: 5174

South Asian (SAS) AF: 0.320 AC: 1541 AN: 4822

European-Finnish (FIN) AF: 0.385 AC: 4067 AN: 10574

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23650 AN: 67982

Other (OTH) AF: 0.408 AC: 862 AN: 2114

Alfa AF: 0.369 Hom.: 33977

Bravo AF: 0.418

Asia WGS AF: 0.487 AC: 1695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.0
DANN	Benign	0.63
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs4734754; hg19: chr8-105278802;