5-53346682-C-T

Variant names:

• chr5-53346682-C-T
• rs37790

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 0.659 in 149,584 control chromosomes in the GnomAD database, including 32,608 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 0.66 (32608 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.659 AC: 98564 AN: 149486 Hom.: 32570 Cov.: 24

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.659 AC: 98648 AN: 149584 Hom.: 32608 Cov.: 24 AF XY: 0.656 AC XY: 47775 AN XY: 72858

African (AFR) AF: 0.700 AC: 28363 AN: 40532

American (AMR) AF: 0.662 AC: 9927 AN: 14994

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2194 AN: 3450

East Asian (EAS) AF: 0.543 AC: 2714 AN: 4996

South Asian (SAS) AF: 0.474 AC: 2218 AN: 4682

European-Finnish (FIN) AF: 0.675 AC: 6823 AN: 10106

Middle Eastern (MID) AF: 0.603 AC: 175 AN: 290

European-Non Finnish (NFE) AF: 0.653 AC: 44133 AN: 67554

Other (OTH) AF: 0.655 AC: 1356 AN: 2070

Alfa AF: 0.653 Hom.: 4039

Bravo AF: 0.670

Asia WGS AF: 0.509 AC: 1769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.043
DANN	Benign	0.79
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs37790; hg19: chr5-52642512;