3-55460051-C-T

Variant names:

• chr3-55460051-C-T
• rs6792802

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 0.489 in 151,720 control chromosomes in the GnomAD database, including 18,506 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 0.49 (18506 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 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: 0.489 AC: 74208 AN: 151600 Hom.: 18497 Cov.: 30

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.489 AC: 74235 AN: 151720 Hom.: 18506 Cov.: 30 AF XY: 0.486 AC XY: 36035 AN XY: 74134

African (AFR) AF: 0.463 AC: 19157 AN: 41346

American (AMR) AF: 0.617 AC: 9417 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1569 AN: 3466

East Asian (EAS) AF: 0.665 AC: 3404 AN: 5116

South Asian (SAS) AF: 0.392 AC: 1883 AN: 4808

European-Finnish (FIN) AF: 0.411 AC: 4339 AN: 10552

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32723 AN: 67864

Other (OTH) AF: 0.507 AC: 1064 AN: 2100

Alfa AF: 0.440 Hom.: 3200

Bravo AF: 0.508

Asia WGS AF: 0.499 AC: 1732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.51
DANN	Benign	0.41
PhyloP100		-0.17

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6792802; hg19: chr3-55494079;