rs2240466

Variant names:

• chr7-73441939-G-A
• rs2240466
• NM_032408.4:c.*15+242C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-73441939-G-A
• chr7-73441939-G-C
• chr7-73441939-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001370402.1(BAZ1B):​c.*257C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 497,894 control chromosomes in the GnomAD database, including 3,012 homozygotes. 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: 𝑓 0.092 (781 hom., cov: 32)
  • Exomes 𝑓: 0.11 (2231 hom.)
• Consequence: BAZ1B NM_001370402.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.36
• Publications: 59 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

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+242C>T		intron	N/A	NP_115784.1	Q9UIG0-1
	BAZ1B	NM_001370402.1		c.*257C>T		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+242C>T		intron	N/A	ENSP00000342434.4	Q9UIG0-1
	BAZ1B	ENST00000404251.1	TSL:2	c.*257C>T		3_prime_UTR	Exon 19 of 19	ENSP00000385442.1	Q9UIG0-1

Frequencies

GnomAD3 genomes AF: 0.0923 AC: 14044 AN: 152074 Hom.: 780 Cov.: 32

Gnomad AFR AF: 0.0420

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0723

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0991

Gnomad SAS AF: 0.0947

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.0859

GnomAD4 exome AF: 0.108 AC: 37367 AN: 345702 Hom.: 2231 Cov.: 0 AF XY: 0.109 AC XY: 19464 AN XY: 179304

African (AFR) AF: 0.0379 AC: 387 AN: 10202

American (AMR) AF: 0.0638 AC: 764 AN: 11970

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 1203 AN: 11272

East Asian (EAS) AF: 0.0996 AC: 2598 AN: 26092

South Asian (SAS) AF: 0.0938 AC: 2371 AN: 25278

European-Finnish (FIN) AF: 0.123 AC: 3069 AN: 24986

Middle Eastern (MID) AF: 0.122 AC: 193 AN: 1586

European-Non Finnish (NFE) AF: 0.115 AC: 24640 AN: 213390

Other (OTH) AF: 0.102 AC: 2142 AN: 20926

GnomAD4 genome AF: 0.0923 AC: 14052 AN: 152192 Hom.: 781 Cov.: 32 AF XY: 0.0921 AC XY: 6855 AN XY: 74406

African (AFR) AF: 0.0419 AC: 1740 AN: 41536

American (AMR) AF: 0.0721 AC: 1103 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 380 AN: 3468

East Asian (EAS) AF: 0.0995 AC: 515 AN: 5176

South Asian (SAS) AF: 0.0950 AC: 459 AN: 4830

European-Finnish (FIN) AF: 0.118 AC: 1246 AN: 10588

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8323 AN: 67984

Other (OTH) AF: 0.0897 AC: 189 AN: 2106

Alfa AF: 0.106 Hom.: 3315

Bravo AF: 0.0839

Asia WGS AF: 0.0980 AC: 342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.16
DANN	Benign	0.62
PhyloP100		-3.4
Mutation Taster		=100/0	polymorphism (auto)

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: rs2240466; hg19: chr7-72856269;