rs7548758

chr1-40257003-C-G

Variant summary

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

The ENST00000567508.2(ZMPSTE24-DT):n.969G>C 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 0.103 in 152,152 control chromosomes in the GnomAD database, including 899 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 0.10 (899 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ZMPSTE24-DT ENST00000567508.2 non_coding_transcript_exon
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 0.0500

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=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZMPSTE24-DT	ENST00000567508.2	n.969G>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15697 AN: 152032 Hom.: 897 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0565

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0930

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0894

Gnomad OTH AF: 0.0960

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: 0.103 AC: 15727 AN: 152152 Hom.: 899 Cov.: 33 AF XY: 0.105 AC XY: 7781 AN XY: 74378

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.0565

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.0930

Gnomad4 NFE AF: 0.0894

Gnomad4 OTH AF: 0.0992

Alfa AF: 0.0905 Hom.: 69

Bravo AF: 0.106

Asia WGS AF: 0.139 AC: 484 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	-0.61
Cadd	Benign	12
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7548758; hg19: chr1-40722675;