rs4843747

chr16-87957445-A-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BANP	NM_001386991.1	c.-69+5930A>C		intron_variant		ENST00000682872.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BANP	ENST00000682872.1	c.-69+5930A>C		intron_variant			NM_001386991.1

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

Gnomad4 AFR AF: 0.948

Gnomad4 AMR AF: 0.816

Gnomad4 ASJ AF: 0.835

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.757

Gnomad4 NFE AF: 0.786

Gnomad4 OTH AF: 0.842

Alfa AF: 0.797 Hom.: 103735

Bravo AF: 0.839

Asia WGS AF: 0.730 AC: 2535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.38
Dann	Benign	0.38
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

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: rs4843747; hg19: chr16-87991051;