chr3-55076280-T-G

Variant names:

• chr3-55076280-T-G
• rs358079

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 0.306 in 151,966 control chromosomes in the GnomAD database, including 7,495 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 0.31 (7495 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.373 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: 0.306 AC: 46484 AN: 151848 Hom.: 7483 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.306 AC: 46525 AN: 151966 Hom.: 7495 Cov.: 32 AF XY: 0.310 AC XY: 23041 AN XY: 74280

African (AFR) AF: 0.226 AC: 9390 AN: 41464

American (AMR) AF: 0.381 AC: 5821 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 985 AN: 3472

East Asian (EAS) AF: 0.284 AC: 1466 AN: 5154

South Asian (SAS) AF: 0.318 AC: 1529 AN: 4814

European-Finnish (FIN) AF: 0.381 AC: 4011 AN: 10540

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22359 AN: 67940

Other (OTH) AF: 0.291 AC: 613 AN: 2104

Alfa AF: 0.302 Hom.: 3175

Bravo AF: 0.300

Asia WGS AF: 0.317 AC: 1105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.021
DANN	Benign	0.42
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs358079; hg19: chr3-55110307;