14-34874538-C-T

Variant names:

• chr14-34874538-C-T
• NM_013448.3:c.67G>A

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4 BS2

The NM_013448.3(BAZ1A):​c.67G>A​(p.Glu23Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000343 in 1,459,792 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E23Q) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.0000034 (0 hom.)
• Consequence: BAZ1A NM_013448.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.81

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)

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.28775907).
• BS2: High AC in GnomAdExome4 at 5 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAZ1A	NM_013448.3	c.67G>A	p.Glu23Lys	missense_variant	Exon 2 of 27	ENST00000360310.6	NP_038476.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAZ1A	ENST00000360310.6	c.67G>A	p.Glu23Lys	missense_variant	Exon 2 of 27	1	NM_013448.3	ENSP00000353458.1
BAZ1A	ENST00000382422.6	c.67G>A	p.Glu23Lys	missense_variant	Exon 1 of 26	1		ENSP00000371859.2
BAZ1A	ENST00000358716.8	c.67G>A	p.Glu23Lys	missense_variant	Exon 2 of 26	1		ENSP00000351555.4
BAZ1A-AS1	ENST00000557373.1	n.196C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000343 AC: 5 AN: 1459792 Hom.: 0 Cov.: 31 AF XY: 0.00000551 AC XY: 4 AN XY: 726248

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: 0.00000450

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.59
BayesDel_addAF	Benign	-0.048	T
BayesDel_noAF	Benign	-0.31
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.076	.;T;T
Eigen	Benign	-0.32
Eigen_PC	Benign	-0.23
FATHMM_MKL	Benign	0.32	N
LIST_S2	Uncertain	0.93	D;.;D
M_CAP	Pathogenic	0.63	D
MetaRNN	Benign	0.29	T;T;T
MetaSVM	Benign	-0.83	T
MutationAssessor	Benign	1.9	L;L;L
PrimateAI	Pathogenic	0.85	D
PROVEAN	Benign	-2.2	N;N;N
REVEL	Benign	0.14
Sift	Uncertain	0.018	D;D;D
Sift4G	Uncertain	0.023	D;D;D
Polyphen		0.030	B;B;B
Vest4		0.29
MutPred		0.66		Gain of methylation at E23 (P = 0.0014);Gain of methylation at E23 (P = 0.0014);Gain of methylation at E23 (P = 0.0014);
MVP		0.55
MPC		0.33
ClinPred		0.87	D
GERP RS		2.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.41
gMVP		0.70

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr14-35343744;