rs926830

Positions:

• chr1-40257123-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZMPSTE24-DT	ENST00000567508.2	n.849C>T		non_coding_transcript_exon_variant	1/1

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

not provided, no classification provided

literature only

ZMPSTE24 homepage - Leiden Muscular Dystrophy pages

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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;