5-58461556-T-C

Variant names:

• chr5-58461556-T-C
• rs702720

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 0.871 in 152,214 control chromosomes in the GnomAD database, including 58,132 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 0.87 (58132 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.958 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: 0.871 AC: 132538 AN: 152096 Hom.: 58080 Cov.: 31

Gnomad AFR AF: 0.966

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.822

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.871 AC: 132642 AN: 152214 Hom.: 58132 Cov.: 31 AF XY: 0.870 AC XY: 64758 AN XY: 74412

African (AFR) AF: 0.966 AC: 40145 AN: 41552

American (AMR) AF: 0.894 AC: 13671 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 2849 AN: 3470

East Asian (EAS) AF: 0.921 AC: 4764 AN: 5174

South Asian (SAS) AF: 0.765 AC: 3691 AN: 4826

European-Finnish (FIN) AF: 0.824 AC: 8713 AN: 10576

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.822 AC: 55868 AN: 68006

Other (OTH) AF: 0.868 AC: 1831 AN: 2110

Alfa AF: 0.806 Hom.: 2738

Bravo AF: 0.885

Asia WGS AF: 0.839 AC: 2917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.48
DANN	Benign	0.33
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs702720; hg19: chr5-57757383;