chr14-34874538-C-G

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2

The NM_013448.3(BAZ1A):​c.67G>C​(p.Glu23Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000281 in 1,459,792 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 0.000028 ( 0 hom. )

Consequence

BAZ1A
NM_013448.3 missense

Scores

2
2
15

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.81
Variant links:
Genes affected
BAZ1A (HGNC:960): (bromodomain adjacent to zinc finger domain 1A) The BAZ1A gene encodes the accessory subunit of the ATP-dependent chromatin assembly factor (ACF), a member of the ISWI ('imitation switch') family of chromatin remodeling complexes (summarized by Racki et al., 2009 [PubMed 20033039]).[supplied by OMIM, Apr 2010]
BAZ1A-AS1 (HGNC:55440): (BAZ1A antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.26579326).
BS2
High AC in GnomAdExome4 at 41 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BAZ1ANM_013448.3 linkc.67G>C p.Glu23Gln missense_variant Exon 2 of 27 ENST00000360310.6 NP_038476.2 Q9NRL2-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BAZ1AENST00000360310.6 linkc.67G>C p.Glu23Gln missense_variant Exon 2 of 27 1 NM_013448.3 ENSP00000353458.1 Q9NRL2-1
BAZ1AENST00000382422.6 linkc.67G>C p.Glu23Gln missense_variant Exon 1 of 26 1 ENSP00000371859.2 Q9NRL2-1
BAZ1AENST00000358716.8 linkc.67G>C p.Glu23Gln missense_variant Exon 2 of 26 1 ENSP00000351555.4 Q9NRL2-2
BAZ1A-AS1ENST00000557373.1 linkn.196C>G non_coding_transcript_exon_variant Exon 1 of 1 6

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD3 exomes
AF:
0.00000805
AC:
2
AN:
248534
Hom.:
0
AF XY:
0.00000742
AC XY:
1
AN XY:
134846
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000178
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000281
AC:
41
AN:
1459792
Hom.:
0
Cov.:
31
AF XY:
0.0000248
AC XY:
18
AN XY:
726248
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000369
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
31
ExAC
AF:
0.00000824
AC:
1

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Jun 11, 2021
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.67G>C (p.E23Q) alteration is located in exon 2 (coding exon 1) of the BAZ1A gene. This alteration results from a G to C substitution at nucleotide position 67, causing the glutamic acid (E) at amino acid position 23 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.38
BayesDel_addAF
Benign
-0.072
T
BayesDel_noAF
Benign
-0.33
CADD
Uncertain
23
DANN
Benign
0.96
DEOGEN2
Benign
0.058
.;T;T
Eigen
Benign
-0.29
Eigen_PC
Benign
-0.21
FATHMM_MKL
Benign
0.37
N
LIST_S2
Uncertain
0.88
D;.;D
M_CAP
Pathogenic
0.54
D
MetaRNN
Benign
0.27
T;T;T
MetaSVM
Benign
-0.87
T
MutationAssessor
Benign
1.7
L;L;L
PrimateAI
Pathogenic
0.79
T
PROVEAN
Benign
-1.7
N;N;N
REVEL
Benign
0.12
Sift
Benign
0.091
T;T;T
Sift4G
Benign
0.21
T;T;T
Polyphen
0.13
B;B;B
Vest4
0.33
MutPred
0.62
Gain of ubiquitination at K28 (P = 0.0773);Gain of ubiquitination at K28 (P = 0.0773);Gain of ubiquitination at K28 (P = 0.0773);
MVP
0.60
MPC
0.30
ClinPred
0.23
T
GERP RS
2.1
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.30
gMVP
0.59

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs756026403; hg19: chr14-35343744; API