16-88017955-C-T

Variant names:

• chr16-88017955-C-T
• rs9936008
• NM_001386991.1:c.656-473C>T

Variant summary

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

The NM_001386991.1(BANP):​c.656-473C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 151,896 control chromosomes in the GnomAD database, including 35,008 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 0.66 (35008 hom., cov: 30)
• Consequence: BANP NM_001386991.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 5 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BANP	NM_001386991.1	c.656-473C>T		intron_variant	Intron 6 of 13	ENST00000682872.1	NP_001373920.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BANP	ENST00000682872.1	c.656-473C>T		intron_variant	Intron 6 of 13		NM_001386991.1	ENSP00000507916.1
BANP	ENST00000626016.2	c.557-473C>T		intron_variant	Intron 5 of 12	2		ENSP00000487304.1
BANP	ENST00000393208.6	c.539-473C>T		intron_variant	Intron 5 of 12	2		ENSP00000376903.2
BANP	ENST00000355022.8	c.539-473C>T		intron_variant	Intron 5 of 11	1		ENSP00000347125.4

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99701 AN: 151778 Hom.: 35005 Cov.: 30

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.657 AC: 99735 AN: 151896 Hom.: 35008 Cov.: 30 AF XY: 0.653 AC XY: 48501 AN XY: 74274

African (AFR) AF: 0.409 AC: 16941 AN: 41390

American (AMR) AF: 0.613 AC: 9363 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2694 AN: 3470

East Asian (EAS) AF: 0.533 AC: 2745 AN: 5154

South Asian (SAS) AF: 0.751 AC: 3584 AN: 4772

European-Finnish (FIN) AF: 0.735 AC: 7771 AN: 10572

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.799 AC: 54281 AN: 67960

Other (OTH) AF: 0.653 AC: 1376 AN: 2106

Alfa AF: 0.639 Hom.: 3505

Bravo AF: 0.631

Asia WGS AF: 0.621 AC: 2164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.48
DANN	Benign	0.54
PhyloP100		-1.6
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: rs9936008; hg19: chr16-88051561;