rs11117358

chr16-88071447-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001386991.1(BANP):c.1378-622T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 456,044 control chromosomes in the GnomAD database, including 13,921 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 0.22 (4009 hom., cov: 33)
  • Exomes 𝑓: 0.25 (9912 hom.)
• Consequence: BANP NM_001386991.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24

Genes affected

BANP (HGNC:13450): (BTG3 associated nuclear protein) This gene encodes a protein that binds to matrix attachment regions. The protein forms a complex with p53 and negatively regulates p53 transcription, and functions as a tumor suppressor and cell cycle regulator. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BANP	NM_001386991.1	c.1378-622T>A		intron_variant		ENST00000682872.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BANP	ENST00000682872.1	c.1378-622T>A		intron_variant			NM_001386991.1

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33893 AN: 152052 Hom.: 4005 Cov.: 33

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.210

GnomAD3 exomes AF: 0.247 AC: 33393 AN: 135042 Hom.: 4192 AF XY: 0.250 AC XY: 18389 AN XY: 73474

Gnomad AFR exome AF: 0.145

Gnomad AMR exome AF: 0.256

Gnomad ASJ exome AF: 0.254

Gnomad EAS exome AF: 0.245

Gnomad SAS exome AF: 0.276

Gnomad FIN exome AF: 0.249

Gnomad NFE exome AF: 0.245

Gnomad OTH exome AF: 0.220

GnomAD4 exome AF: 0.253 AC: 76777 AN: 303874 Hom.: 9912 Cov.: 0 AF XY: 0.257 AC XY: 44396 AN XY: 173056

Gnomad4 AFR exome AF: 0.148

Gnomad4 AMR exome AF: 0.255

Gnomad4 ASJ exome AF: 0.253

Gnomad4 EAS exome AF: 0.243

Gnomad4 SAS exome AF: 0.276

Gnomad4 FIN exome AF: 0.252

Gnomad4 NFE exome AF: 0.253

Gnomad4 OTH exome AF: 0.234

GnomAD4 genome AF: 0.223 AC: 33916 AN: 152170 Hom.: 4009 Cov.: 33 AF XY: 0.225 AC XY: 16752 AN XY: 74380

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.212

Alfa AF: 0.244 Hom.: 794

Bravo AF: 0.215

Asia WGS AF: 0.257 AC: 894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.57
Dann	Benign	0.81

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

Other links and lift over

dbSNP: rs11117358; hg19: chr16-88105053; COSMIC: COSV53735063;