chr1-40257003-C-G

Variant names:

• chr1-40257003-C-G
• rs7548758
• ENST00000567508.3:n.992G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000567508.3(ZMPSTE24-DT):​n.992G>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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.10 (899 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ZMPSTE24-DT ENST00000567508.3 non_coding_transcript_exon
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 0.0500
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZMPSTE24-DT	ENST00000567508.3	n.992G>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.103 AC: 15727 AN: 152152 Hom.: 899 Cov.: 33 AF XY: 0.105 AC XY: 7781 AN XY: 74378

African (AFR) AF: 0.110 AC: 4581 AN: 41508

American (AMR) AF: 0.135 AC: 2069 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0565 AC: 196 AN: 3470

East Asian (EAS) AF: 0.154 AC: 799 AN: 5178

South Asian (SAS) AF: 0.153 AC: 739 AN: 4818

European-Finnish (FIN) AF: 0.0930 AC: 984 AN: 10584

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0894 AC: 6080 AN: 67990

Other (OTH) AF: 0.0992 AC: 210 AN: 2116

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

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ZMPSTE24 homepage - Leiden Muscular Dystrophy pages

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	12
DANN	Benign	0.82
PhyloP100		0.050

Splicing

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

Other links and lift over

dbSNP: rs7548758; hg19: chr1-40722675;