rs12378647

chr9-119239436-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.580-676C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 152,126 control chromosomes in the GnomAD database, including 38,176 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 0.71 (38176 hom., cov: 33)
• Consequence: BRINP1 NM_014618.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134

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 (EAS) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRINP1	NM_014618.3	c.580-676C>T		intron_variant		ENST00000265922.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRINP1	ENST00000265922.8	c.580-676C>T		intron_variant		1	NM_014618.3	P1
BRINP1	ENST00000373964.2	c.580-676C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107354 AN: 152008 Hom.: 38143 Cov.: 33

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.706 AC: 107446 AN: 152126 Hom.: 38176 Cov.: 33 AF XY: 0.706 AC XY: 52537 AN XY: 74392

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.756

Gnomad4 ASJ AF: 0.698

Gnomad4 EAS AF: 0.763

Gnomad4 SAS AF: 0.751

Gnomad4 FIN AF: 0.648

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.715

Alfa AF: 0.681 Hom.: 50487

Bravo AF: 0.715

Asia WGS AF: 0.765 AC: 2663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.85
Dann	Benign	0.20

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: rs12378647; hg19: chr9-122001714;