rs926830

Variant names:

• chr1-40257123-G-A
• rs926830
• ENST00000567508.2:n.849C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000567508.2(ZMPSTE24-DT):​n.849C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,062 control chromosomes in the GnomAD database, including 4,846 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

• Frequency:
  • Genomes: 𝑓 0.25 (4846 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ZMPSTE24-DT ENST00000567508.2 non_coding_transcript_exon
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 0.868

Genes affected

ZMPSTE24-DT (HGNC:55402): (ZMPSTE24 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 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
ZMPSTE24-DT	ENST00000567508.2	n.849C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37898 AN: 151944 Hom.: 4847 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.240

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.249 AC: 37893 AN: 152062 Hom.: 4846 Cov.: 32 AF XY: 0.249 AC XY: 18478 AN XY: 74316

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.239

Alfa AF: 0.254 Hom.: 8392

Bravo AF: 0.241

Asia WGS AF: 0.215 AC: 746 AN: 3478

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

not provided Other:1

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ZMPSTE24 homepage - Leiden Muscular Dystrophy pages

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	12
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs926830; hg19: chr1-40722795; COSMIC: COSV65638920;