5-58888234-T-C

Variant names:

• chr5-58888234-T-C
• rs10472076

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 0.333 in 152,012 control chromosomes in the GnomAD database, including 8,587 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 0.33 (8587 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.374 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: 0.333 AC: 50637 AN: 151890 Hom.: 8579 Cov.: 31

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.333 AC: 50662 AN: 152012 Hom.: 8587 Cov.: 31 AF XY: 0.331 AC XY: 24621 AN XY: 74296

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.349

Alfa AF: 0.352 Hom.: 10442

Bravo AF: 0.323

Asia WGS AF: 0.281 AC: 978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.56
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10472076; hg19: chr5-58184061;