9-119297431-T-C

Variant names:

• chr9-119297431-T-C
• rs4837628
• NM_014618.3:c.218+15707A>G

Variant summary

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

The NM_014618.3(BRINP1):​c.218+15707A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 151,866 control chromosomes in the GnomAD database, including 18,058 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 0.48 (18058 hom., cov: 31)
• Consequence: BRINP1 NM_014618.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.846
• Publications: 15 publications found

Genes affected

BRINP1 (HGNC:2687): (BMP/retinoic acid inducible neural specific 1) This gene is located within a chromosomal region that shows loss of heterozygosity in some bladder cancers. It contains a 5' CpG island that may be a frequent target of hypermethylation, and it may undergo hypermethylation-based silencing in some bladder cancers. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014618.3. 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
	BRINP1	NM_014618.3	MANE Select	c.218+15707A>G		intron	N/A	NP_055433.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRINP1	ENST00000265922.8	TSL:1 MANE Select	c.218+15707A>G		intron	N/A	ENSP00000265922.2
	BRINP1	ENST00000373964.2	TSL:1	c.218+15707A>G		intron	N/A	ENSP00000363075.1

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72312 AN: 151748 Hom.: 18022 Cov.: 31

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.477 AC: 72394 AN: 151866 Hom.: 18058 Cov.: 31 AF XY: 0.473 AC XY: 35102 AN XY: 74222

African (AFR) AF: 0.613 AC: 25368 AN: 41370

American (AMR) AF: 0.426 AC: 6504 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1372 AN: 3470

East Asian (EAS) AF: 0.337 AC: 1736 AN: 5154

South Asian (SAS) AF: 0.319 AC: 1535 AN: 4812

European-Finnish (FIN) AF: 0.456 AC: 4808 AN: 10546

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29558 AN: 67928

Other (OTH) AF: 0.443 AC: 936 AN: 2114

Alfa AF: 0.437 Hom.: 43942

Bravo AF: 0.483

Asia WGS AF: 0.370 AC: 1288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.78
DANN	Benign	0.54
PhyloP100		-0.85
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: rs4837628; hg19: chr9-122059709;