16-87957445-A-C

Variant names:

• chr16-87957445-A-C
• rs4843747
• NM_001386991.1:c.-69+5930A>C

Variant summary

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

The NM_001386991.1(BANP):​c.-69+5930A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.826 in 152,208 control chromosomes in the GnomAD database, including 52,550 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 0.83 (52550 hom., cov: 32)
• Consequence: BANP NM_001386991.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.775
• Publications: 17 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.94 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BANP	NM_001386991.1	MANE Select	c.-69+5930A>C		intron	N/A	NP_001373920.1
	BANP	NM_001386992.1		c.-69+5930A>C		intron	N/A	NP_001373921.1
	BANP	NM_001384928.1		c.-69+6518A>C		intron	N/A	NP_001371857.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BANP	ENST00000682872.1	MANE Select	c.-69+5930A>C		intron	N/A	ENSP00000507916.1
	BANP	ENST00000626016.2	TSL:2	c.-69+5930A>C		intron	N/A	ENSP00000487304.1
	BANP	ENST00000393208.6	TSL:2	c.-69+5930A>C		intron	N/A	ENSP00000376903.2

Frequencies

GnomAD3 genomes AF: 0.826 AC: 125676 AN: 152090 Hom.: 52494 Cov.: 32

Gnomad AFR AF: 0.948

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.842

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.826 AC: 125794 AN: 152208 Hom.: 52550 Cov.: 32 AF XY: 0.820 AC XY: 61041 AN XY: 74408

African (AFR) AF: 0.948 AC: 39410 AN: 41560

American (AMR) AF: 0.816 AC: 12488 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.835 AC: 2899 AN: 3470

East Asian (EAS) AF: 0.729 AC: 3770 AN: 5168

South Asian (SAS) AF: 0.655 AC: 3160 AN: 4824

European-Finnish (FIN) AF: 0.757 AC: 8009 AN: 10578

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.786 AC: 53434 AN: 67988

Other (OTH) AF: 0.842 AC: 1782 AN: 2116

Alfa AF: 0.806 Hom.: 154714

Bravo AF: 0.839

Asia WGS AF: 0.730 AC: 2535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.38
DANN	Benign	0.38
PhyloP100		-0.78
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
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: rs4843747; hg19: chr16-87991051;