rs926830

Variant names:

• chr1-40257123-G-A
• rs926830
• ENST00000567508.3:n.872C>T

Variant summary

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

The ENST00000567508.3(ZMPSTE24-DT):​n.872C>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 ENST00000567508.3 non_coding_transcript_exon
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 0.868
• Publications: 3 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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000567508.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZMPSTE24-DT	ENST00000567508.3	TSL:6	n.872C>T		non_coding_transcript_exon	Exon 1 of 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

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

African (AFR) AF: 0.252 AC: 10449 AN: 41452

American (AMR) AF: 0.179 AC: 2734 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 753 AN: 3468

East Asian (EAS) AF: 0.244 AC: 1265 AN: 5180

South Asian (SAS) AF: 0.178 AC: 860 AN: 4826

European-Finnish (FIN) AF: 0.295 AC: 3112 AN: 10538

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 18046 AN: 67988

Other (OTH) AF: 0.239 AC: 504 AN: 2106

Alfa AF: 0.256 Hom.: 19518

Bravo AF: 0.241

Asia WGS AF: 0.215 AC: 746 AN: 3478

ClinVar

ClinVar submissions

Significance: not provided

Revision: no classification provided

Pathogenic	VUS	Benign	Condition
-	-	-	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	12
DANN	Benign	0.67
PhyloP100		0.87

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs926830;

hg19: chr1-40722795;

COSMIC: COSV65638920;