7-73442100-T-G

Variant names:

• chr7-73442100-T-G
• rs1178979
• NM_032408.4:c.*15+81A>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001370402.1(BAZ1B):​c.*96A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000016 in 810,010 control chromosomes in the GnomAD database, with no homozygous occurrence. There is a variant allele frequency bias in the population database for this variant (GnomAdExome4), which may indicate mosaicism or somatic mutations in the reference population data. 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: 30)
  • Exomes 𝑓: 0.000016 (0 hom.)
• Consequence: BAZ1B NM_001370402.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45
• Publications: 0 publications found

Genes affected

BAZ1B (HGNC:961): (bromodomain adjacent to zinc finger domain 1B) This gene encodes a member of the bromodomain protein family. The bromodomain is a structural motif characteristic of proteins involved in chromatin-dependent regulation of transcription. This gene is deleted in Williams-Beuren syndrome, a developmental disorder caused by deletion of multiple genes at 7q11.23. [provided by RefSeq, Jul 2008]

BAZ1B Gene-Disease associations (from GenCC):

• autism spectrum disorder

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370402.1. 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
	BAZ1B	NM_032408.4	MANE Select	c.*15+81A>C		intron	N/A	NP_115784.1	Q9UIG0-1
	BAZ1B	NM_001370402.1		c.*96A>C		3_prime_UTR	Exon 19 of 19	NP_001357331.1	Q9UIG0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAZ1B	ENST00000339594.9	TSL:1 MANE Select	c.*15+81A>C		intron	N/A	ENSP00000342434.4	Q9UIG0-1
	BAZ1B	ENST00000404251.1	TSL:2	c.*96A>C		3_prime_UTR	Exon 19 of 19	ENSP00000385442.1	Q9UIG0-1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome AF: 0.0000160 AC: 13 AN: 810010 Hom.: 0 Cov.: 11 AF XY: 0.0000145 AC XY: 6 AN XY: 414820

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 19112

American (AMR) AF: 0.00 AC: 0 AN: 28440

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16386

East Asian (EAS) AF: 0.00 AC: 0 AN: 36040

South Asian (SAS) AF: 0.0000169 AC: 1 AN: 59286

European-Finnish (FIN) AF: 0.0000292 AC: 1 AN: 34220

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2666

European-Non Finnish (NFE) AF: 0.0000191 AC: 11 AN: 575896

Other (OTH) AF: 0.00 AC: 0 AN: 37964

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.027
DANN	Benign	0.53
PhyloP100		-2.5

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

Other links and lift over

dbSNP: rs1178979; hg19: chr7-72856430;