GeneBe

8-80487910-G-A

Variant names:

Variant summary

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

The NM_001105539.3(ZBTB10):​c.972+128G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000104 in 963,750 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 0.0000010 ( 0 hom. )

Consequence

ZBTB10
NM_001105539.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.239

Publications

2 publications found
Variant links:
Genes affected
ZBTB10 (HGNC:30953): (zinc finger and BTB domain containing 10) Predicted to enable RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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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=-0.79).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZBTB10NM_001105539.3 linkc.972+128G>A intron_variant Intron 1 of 5 ENST00000455036.8 NP_001099009.1 Q96DT7-1
ZBTB10NM_023929.5 linkc.972+128G>A intron_variant Intron 1 of 6 NP_076418.3 Q96DT7-2Q9H9H3
ZBTB10NM_001277145.2 linkc.96+2031G>A intron_variant Intron 1 of 5 NP_001264074.1 Q96DT7-4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZBTB10ENST00000455036.8 linkc.972+128G>A intron_variant Intron 1 of 5 2 NM_001105539.3 ENSP00000412036.3 Q96DT7-1
ZBTB10ENST00000430430.5 linkc.972+128G>A intron_variant Intron 2 of 6 5 ENSP00000387462.1 Q96DT7-1
ZBTB10ENST00000426744.5 linkc.972+128G>A intron_variant Intron 1 of 6 5 ENSP00000416134.2 Q96DT7-2
ZBTB10ENST00000379091.8 linkc.96+2031G>A intron_variant Intron 1 of 5 2 ENSP00000368384.4 Q96DT7-4

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000104
AC:
1
AN:
963750
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
475820
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
21836
American (AMR)
AF:
0.00
AC:
0
AN:
18326
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
16772
East Asian (EAS)
AF:
0.00
AC:
0
AN:
32946
South Asian (SAS)
AF:
0.00
AC:
0
AN:
50932
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
29802
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3050
European-Non Finnish (NFE)
AF:
0.00000134
AC:
1
AN:
747190
Other (OTH)
AF:
0.00
AC:
0
AN:
42896
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
6

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
6.6
DANN
Benign
0.77
PhyloP100
-0.24

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs482951; hg19: chr8-81400145; API