rs1324618

Positions:

• chr9-119305684-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+7454C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 151,844 control chromosomes in the GnomAD database, including 1,194 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 0.11 (1194 hom., cov: 32)
• Consequence: BRINP1 NM_014618.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRINP1	NM_014618.3	c.218+7454C>T		intron_variant		ENST00000265922.8	NP_055433.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRINP1	ENST00000265922.8	c.218+7454C>T		intron_variant		1	NM_014618.3	ENSP00000265922	P1
BRINP1	ENST00000373964.2	c.218+7454C>T		intron_variant		1		ENSP00000363075

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16687 AN: 151726 Hom.: 1186 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0777

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.0593

Gnomad SAS AF: 0.0164

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0784

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.110 AC: 16737 AN: 151844 Hom.: 1194 Cov.: 32 AF XY: 0.111 AC XY: 8220 AN XY: 74194

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.0776

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.0590

Gnomad4 SAS AF: 0.0160

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.0783

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0985 Hom.: 111

Bravo AF: 0.108

Asia WGS AF: 0.0560 AC: 196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.21

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: rs1324618; hg19: chr9-122067962;