rs611199

Variant names:

• chr9-119285698-G-A
• rs611199
• NM_014618.3:c.218+27440C>T

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+27440C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,958 control chromosomes in the GnomAD database, including 7,694 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 0.31 (7694 hom., cov: 32)
• Consequence: BRINP1 NM_014618.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.946
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.341 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRINP1	NM_014618.3	MANE Select	c.218+27440C>T		intron	N/A	NP_055433.2	O60477-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRINP1	ENST00000265922.8	TSL:1 MANE Select	c.218+27440C>T		intron	N/A	ENSP00000265922.2	O60477-1
	BRINP1	ENST00000373964.2	TSL:1	c.218+27440C>T		intron	N/A	ENSP00000363075.1	O60477-2
	BRINP1	ENST00000958983.1		c.218+27440C>T		intron	N/A	ENSP00000629042.1

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47764 AN: 151840 Hom.: 7682 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.315 AC: 47791 AN: 151958 Hom.: 7694 Cov.: 32 AF XY: 0.312 AC XY: 23210 AN XY: 74286

African (AFR) AF: 0.272 AC: 11284 AN: 41438

American (AMR) AF: 0.328 AC: 5011 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 911 AN: 3470

East Asian (EAS) AF: 0.277 AC: 1427 AN: 5144

South Asian (SAS) AF: 0.289 AC: 1387 AN: 4806

European-Finnish (FIN) AF: 0.302 AC: 3190 AN: 10558

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23441 AN: 67966

Other (OTH) AF: 0.297 AC: 628 AN: 2112

Alfa AF: 0.338 Hom.: 4151

Bravo AF: 0.317

Asia WGS AF: 0.299 AC: 1038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.093
DANN	Benign	0.60
PhyloP100		-0.95
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: rs611199; hg19: chr9-122047976;