Variant 9-119167654-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_014618.3(BRINP1):c.1716G>A(p.Ser572Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00642 in 1,614,078 control chromosomes in the GnomAD database, including 52 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0055 ( 5 hom., cov: 32)

Exomes 𝑓: 0.0065 ( 47 hom. )

Consequence

BRINP1
NM_014618.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -5.34

Variant links:

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]

BRINP1 links:

BRINP1 (HGNC:):

BRINP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 9-119167654-C-T is Benign according to our data. Variant chr9-119167654-C-T is described in ClinVar as [Benign]. Clinvar id is 771880.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-5.34 with no splicing effect.

BS2

High AC in GnomAd4 at 839 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRINP1	NM_014618.3 linkuse as main transcript	c.1716G>A	p.Ser572Ser	synonymous_variant	8/8	ENST00000265922.8	NP_055433.2	O60477-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRINP1	ENST00000265922.8 linkuse as main transcript	c.1716G>A	p.Ser572Ser	synonymous_variant	8/8	1	NM_014618.3	ENSP00000265922.2		O60477-1
BRINP1	ENST00000482797.1 linkuse as main transcript	n.169-13793G>A		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.00553

AC:

841

AN:

152150

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00133

Gnomad AMI

AF:

0.0330

Gnomad AMR

AF:

0.00635

Gnomad ASJ

AF:

0.0213

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000415

Gnomad FIN

AF:

0.00734

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.00714

Gnomad OTH

AF:

0.00479

GnomAD3 exomes

AF:

0.00586

AC:

1462

AN:

249688

Hom.:

AF XY:

0.00598

AC XY:

809

AN XY:

135212

show subpopulations

Gnomad AFR exome

AF:

0.000889

Gnomad AMR exome

AF:

0.00393

Gnomad ASJ exome

AF:

0.0195

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000621

Gnomad FIN exome

AF:

0.00813

Gnomad NFE exome

AF:

0.00781

Gnomad OTH exome

AF:

0.00688

GnomAD4 exome

AF:

0.00652

AC:

9529

AN:

1461810

Hom.:

Cov.:

AF XY:

0.00644

AC XY:

4681

AN XY:

727212

show subpopulations

Gnomad4 AFR exome

AF:

0.000986

Gnomad4 AMR exome

AF:

0.00382

Gnomad4 ASJ exome

AF:

0.0192

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.000649

Gnomad4 FIN exome

AF:

0.00918

Gnomad4 NFE exome

AF:

0.00703

Gnomad4 OTH exome

AF:

0.00666

GnomAD4 genome

AF:

0.00551

AC:

839

AN:

152268

Hom.:

Cov.:

AF XY:

0.00556

AC XY:

414

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.00132

Gnomad4 AMR

AF:

0.00634

Gnomad4 ASJ

AF:

0.0213

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000415

Gnomad4 FIN

AF:

0.00734

Gnomad4 NFE

AF:

0.00714

Gnomad4 OTH

AF:

0.00474

Alfa

AF:

0.00696

Hom.:

Bravo

AF:

0.00516

EpiCase

AF:

0.00807

EpiControl

AF:

0.00794

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Aug 01, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.64

DANN

Benign

0.71

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over