5-73991586-C-A

Variant names:

• chr5-73991586-C-A
• rs255592

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 0.732 in 152,018 control chromosomes in the GnomAD database, including 40,961 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 0.73 (40961 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.960

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.8 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: 0.732 AC: 111217 AN: 151900 Hom.: 40924 Cov.: 32

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.732 AC: 111309 AN: 152018 Hom.: 40961 Cov.: 32 AF XY: 0.734 AC XY: 54507 AN XY: 74296

Gnomad4 AFR AF: 0.774

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.762

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.730

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.750

Alfa AF: 0.716 Hom.: 78144

Bravo AF: 0.746

Asia WGS AF: 0.642 AC: 2231 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.65
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs255592; hg19: chr5-73287411;