rs2055451

Variant names:

• chr3-79792979-G-T
• rs2055451

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 0.299 in 151,844 control chromosomes in the GnomAD database, including 6,882 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 0.30 (6882 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 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: 0.299 AC: 45371 AN: 151724 Hom.: 6876 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.299 AC: 45411 AN: 151844 Hom.: 6882 Cov.: 32 AF XY: 0.298 AC XY: 22126 AN XY: 74214

African (AFR) AF: 0.340 AC: 14102 AN: 41416

American (AMR) AF: 0.283 AC: 4322 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 686 AN: 3464

East Asian (EAS) AF: 0.325 AC: 1678 AN: 5162

South Asian (SAS) AF: 0.308 AC: 1482 AN: 4812

European-Finnish (FIN) AF: 0.264 AC: 2785 AN: 10562

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19459 AN: 67864

Other (OTH) AF: 0.276 AC: 582 AN: 2110

Alfa AF: 0.293 Hom.: 3241

Bravo AF: 0.304

Asia WGS AF: 0.316 AC: 1097 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	15
DANN	Benign	0.37
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs2055451; hg19: chr3-79842129;