5-58461556-T-C

Position:

• chr5-58461556-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;