rs611199

Positions:

• chr9-119285698-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRINP1	NM_014618.3	c.218+27440C>T		intron_variant		ENST00000265922.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRINP1	ENST00000265922.8	c.218+27440C>T		intron_variant		1	NM_014618.3	P1
BRINP1	ENST00000373964.2	c.218+27440C>T		intron_variant		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

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.297

Alfa AF: 0.337 Hom.: 3654

Bravo AF: 0.317

Asia WGS AF: 0.299 AC: 1038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.093
DANN	Benign	0.60

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: rs611199; hg19: chr9-122047976;