rs11117358

Variant names:

• chr16-88071447-T-A
• rs11117358
• NM_001386991.1:c.1378-622T>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate 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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.073).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001386991.1. 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
	BANP	NM_001386991.1	MANE Select	c.1378-622T>A		intron	N/A	NP_001373920.1	A0A804HKG3
	BANP	NM_001386992.1		c.1369-622T>A		intron	N/A	NP_001373921.1
	BANP	NM_001173543.1		c.1345-622T>A		intron	N/A	NP_001167014.1	B3KM38

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BANP	ENST00000682872.1	MANE Select	c.1378-622T>A		intron	N/A	ENSP00000507916.1	A0A804HKG3
	BANP	ENST00000538234.5	TSL:1	c.1312-622T>A		intron	N/A	ENSP00000444352.1	Q8N9N5-7
	BANP	ENST00000626016.2	TSL:2	c.1279-622T>A		intron	N/A	ENSP00000487304.1	Q8N9N5-5

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

GnomAD2 exomes AF: 0.247 AC: 33393 AN: 135042 AF XY: 0.250

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 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

African (AFR) AF: 0.148 AC: 1275 AN: 8614

American (AMR) AF: 0.255 AC: 6962 AN: 27254

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 2727 AN: 10774

East Asian (EAS) AF: 0.243 AC: 2240 AN: 9210

South Asian (SAS) AF: 0.276 AC: 16470 AN: 59724

European-Finnish (FIN) AF: 0.252 AC: 3173 AN: 12602

Middle Eastern (MID) AF: 0.146 AC: 406 AN: 2776

European-Non Finnish (NFE) AF: 0.253 AC: 40194 AN: 158712

Other (OTH) AF: 0.234 AC: 3330 AN: 14208

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

African (AFR) AF: 0.153 AC: 6356 AN: 41540

American (AMR) AF: 0.224 AC: 3424 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 879 AN: 3468

East Asian (EAS) AF: 0.248 AC: 1281 AN: 5168

South Asian (SAS) AF: 0.279 AC: 1344 AN: 4820

European-Finnish (FIN) AF: 0.260 AC: 2747 AN: 10576

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17039 AN: 67980

Other (OTH) AF: 0.212 AC: 447 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.57
DANN	Benign	0.81
PhyloP100		-2.2
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: rs11117358; hg19: chr16-88105053; COSMIC: COSV53735063;