5-58461556-T-C

Variant names:

• chr5-58461556-T-C
• rs702720

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.966

Gnomad4 AMR AF: 0.894

Gnomad4 ASJ AF: 0.821

Gnomad4 EAS AF: 0.921

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.824

Gnomad4 NFE AF: 0.822

Gnomad4 OTH AF: 0.868

Alfa AF: 0.789 Hom.: 2371

Bravo AF: 0.885

Asia WGS AF: 0.839 AC: 2917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs702720; hg19: chr5-57757383;