5-58011534-G-A

Variant names:

• chr5-58011534-G-A
• rs10513134

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 0.0423 in 151,976 control chromosomes in the GnomAD database, including 345 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 0.042 (345 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.154 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0424 AC: 6432 AN: 151858 Hom.: 345 Cov.: 32

Gnomad AFR AF: 0.00861

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.00808

Gnomad EAS AF: 0.0148

Gnomad SAS AF: 0.00415

Gnomad FIN AF: 0.0864

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0375

Gnomad OTH AF: 0.0278

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

GnomAD4 genome AF: 0.0423 AC: 6436 AN: 151976 Hom.: 345 Cov.: 32 AF XY: 0.0469 AC XY: 3487 AN XY: 74274

African (AFR) AF: 0.00859 AC: 356 AN: 41464

American (AMR) AF: 0.159 AC: 2425 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.00808 AC: 28 AN: 3466

East Asian (EAS) AF: 0.0147 AC: 76 AN: 5180

South Asian (SAS) AF: 0.00415 AC: 20 AN: 4820

European-Finnish (FIN) AF: 0.0864 AC: 913 AN: 10568

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0375 AC: 2549 AN: 67926

Other (OTH) AF: 0.0275 AC: 58 AN: 2110

Alfa AF: 0.0301 Hom.: 42

Bravo AF: 0.0477

Asia WGS AF: 0.0200 AC: 70 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.58
DANN	Benign	0.19
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs10513134; hg19: chr5-57307361;