rs10984447

Variant names:

• chr9-119222275-A-G
• rs10984447
• NM_014618.3:c.686-8120T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 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 (NFE) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRINP1	NM_014618.3	c.686-8120T>C		intron_variant	Intron 5 of 7	ENST00000265922.8	NP_055433.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRINP1	ENST00000265922.8	c.686-8120T>C		intron_variant	Intron 5 of 7	1	NM_014618.3	ENSP00000265922.2
BRINP1	ENST00000373964.2	c.686-8120T>C		intron_variant	Intron 5 of 5	1		ENSP00000363075.1

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

African (AFR) AF: 0.0960 AC: 3985 AN: 41532

American (AMR) AF: 0.221 AC: 3362 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 545 AN: 3466

East Asian (EAS) AF: 0.101 AC: 520 AN: 5160

South Asian (SAS) AF: 0.196 AC: 944 AN: 4818

European-Finnish (FIN) AF: 0.185 AC: 1962 AN: 10584

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16784 AN: 67944

Other (OTH) AF: 0.179 AC: 376 AN: 2106

Alfa AF: 0.227 Hom.: 17971

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
PhyloP100		-0.13
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: rs10984447; hg19: chr9-121984553;