chr1-40256236-T-C

Variant names:

• chr1-40256236-T-C
• rs9326050
• ENST00000567508.3:n.*97A>G

Variant summary

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

The ENST00000567508.3(ZMPSTE24-DT):​n.*97A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 152,036 control chromosomes in the GnomAD database, including 25,189 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 0.56 (25189 hom., cov: 31)
• Consequence: ZMPSTE24-DT ENST00000567508.3 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 2 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.726 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.*97A>G		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85406 AN: 151918 Hom.: 25147 Cov.: 31

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.562 AC: 85512 AN: 152036 Hom.: 25189 Cov.: 31 AF XY: 0.568 AC XY: 42244 AN XY: 74312

African (AFR) AF: 0.733 AC: 30390 AN: 41488

American (AMR) AF: 0.508 AC: 7771 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1344 AN: 3462

East Asian (EAS) AF: 0.728 AC: 3760 AN: 5166

South Asian (SAS) AF: 0.648 AC: 3118 AN: 4814

European-Finnish (FIN) AF: 0.541 AC: 5704 AN: 10542

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31944 AN: 67956

Other (OTH) AF: 0.516 AC: 1092 AN: 2116

Alfa AF: 0.521 Hom.: 3491

Bravo AF: 0.567

Asia WGS AF: 0.705 AC: 2454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.72
DANN	Benign	0.48
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9326050; hg19: chr1-40721908; COSMIC: COSV65638917;