GeneBe

10-79065692-G-T

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000456353.5(ZMIZ1-AS1):​n.720+55C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

ZMIZ1-AS1
ENST00000456353.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0290
Variant links:
Genes affected
ZMIZ1-AS1 (HGNC:27433): (ZMIZ1 antisense RNA 1)

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZMIZ1-AS1NR_015429.1 linkn.273+55C>A intron_variant Intron 3 of 7
ZMIZ1-AS1NR_024429.1 linkn.273+55C>A intron_variant Intron 3 of 7
ZMIZ1-AS1NR_024431.2 linkn.273+55C>A intron_variant Intron 3 of 9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZMIZ1-AS1ENST00000440151.3 linkn.171+55C>A intron_variant Intron 2 of 4 3
ZMIZ1-AS1ENST00000456353.5 linkn.720+55C>A intron_variant Intron 3 of 9 2
ZMIZ1-AS1ENST00000665190.1 linkn.106+55C>A intron_variant Intron 2 of 5

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
42
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
22
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
0.00
AC:
0
AN:
2
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
8
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
28
Other (OTH)
AF:
0.00
AC:
0
AN:
4
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
1.2
DANN
Benign
0.33
PhyloP100
0.029

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar for variant 10:79065692 G>T . It may be empty.

Other links and lift over

dbSNP: rs1370562; hg19: chr10-80825449; API