5-58888234-T-C

Variant names:

• chr5-58888234-T-C
• rs10472076

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 0.333 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
• Publications: 67 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.333 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

African (AFR) AF: 0.269 AC: 11167 AN: 41468

American (AMR) AF: 0.311 AC: 4758 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1184 AN: 3466

East Asian (EAS) AF: 0.269 AC: 1391 AN: 5162

South Asian (SAS) AF: 0.270 AC: 1302 AN: 4814

European-Finnish (FIN) AF: 0.374 AC: 3958 AN: 10570

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.378 AC: 25657 AN: 67926

Other (OTH) AF: 0.349 AC: 736 AN: 2108

Alfa AF: 0.353 Hom.: 29840

Bravo AF: 0.323

Asia WGS AF: 0.281 AC: 978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.56
DANN	Benign	0.69
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs10472076; hg19: chr5-58184061;