rs10984447

Positions:

• chr9-119222275-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014618.3(BRINP1):​c.686-8120T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,040 control chromosomes in the GnomAD database, including 3,077 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 0.19 (3077 hom., cov: 32)
• Consequence: BRINP1 NM_014618.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRINP1	NM_014618.3	c.686-8120T>C		intron_variant		ENST00000265922.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRINP1	ENST00000265922.8	c.686-8120T>C		intron_variant		1	NM_014618.3	P1
BRINP1	ENST00000373964.2	c.686-8120T>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28856 AN: 151922 Hom.: 3074 Cov.: 32

Gnomad AFR AF: 0.0959

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.190 AC: 28871 AN: 152040 Hom.: 3077 Cov.: 32 AF XY: 0.187 AC XY: 13877 AN XY: 74322

Gnomad4 AFR AF: 0.0960

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.179

Alfa AF: 0.230 Hom.: 8307

Bravo AF: 0.190

Asia WGS AF: 0.176 AC: 610 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.41
DANN	Benign	0.48

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: rs10984447; hg19: chr9-121984553;