chr16-88017955-C-A

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001386991.1(BANP):​c.656-473C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

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.656-473C>A		intron	N/A	NP_001373920.1	A0A804HKG3
	BANP	NM_001386992.1		c.656-473C>A		intron	N/A	NP_001373921.1
	BANP	NM_001173543.1		c.632-473C>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.656-473C>A		intron	N/A	ENSP00000507916.1	A0A804HKG3
	BANP	ENST00000538234.5	TSL:1	c.656-473C>A		intron	N/A	ENSP00000444352.1	Q8N9N5-7
	BANP	ENST00000626016.2	TSL:2	c.557-473C>A		intron	N/A	ENSP00000487304.1	Q8N9N5-5

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 3505

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.20
DANN	Benign	0.54
PhyloP100		-1.6

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;