Variant chr9-119167448-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_014618.3(BRINP1):c.1922C>T(p.Ser641Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00877 in 1,614,102 control chromosomes in the GnomAD database, including 117 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0073 ( 16 hom., cov: 32)

Exomes 𝑓: 0.0089 ( 101 hom. )

Consequence

BRINP1
NM_014618.3 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 7.76

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 -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0076669157).

BP6

Variant 9-119167448-G-A is Benign according to our data. Variant chr9-119167448-G-A is described in ClinVar as [Benign]. Clinvar id is 774320.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High AC in GnomAd4 at 1108 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRINP1	NM_014618.3 linkuse as main transcript	c.1922C>T	p.Ser641Leu	missense_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.1922C>T	p.Ser641Leu	missense_variant	8/8	1	NM_014618.3	ENSP00000265922.2		O60477-1
BRINP1	ENST00000482797.1 linkuse as main transcript	n.169-13587C>T		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.00728

AC:

1108

AN:

152166

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00162

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00131

Gnomad ASJ

AF:

0.00317

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00228

Gnomad FIN

AF:

0.0188

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0117

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00758

AC:

1904

AN:

251312

Hom.:

AF XY:

0.00740

AC XY:

1005

AN XY:

135826

show subpopulations

Gnomad AFR exome

AF:

0.00111

Gnomad AMR exome

AF:

0.00214

Gnomad ASJ exome

AF:

0.00238

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.00157

Gnomad FIN exome

AF:

0.0197

Gnomad NFE exome

AF:

0.0112

Gnomad OTH exome

AF:

0.00718

GnomAD4 exome

AF:

0.00893

AC:

13048

AN:

1461818

Hom.:

101

Cov.:

AF XY:

0.00892

AC XY:

6488

AN XY:

727208

show subpopulations

Gnomad4 AFR exome

AF:

0.000986

Gnomad4 AMR exome

AF:

0.00212

Gnomad4 ASJ exome

AF:

0.00287

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00194

Gnomad4 FIN exome

AF:

0.0204

Gnomad4 NFE exome

AF:

0.0100

Gnomad4 OTH exome

AF:

0.00742

GnomAD4 genome

AF:

0.00728

AC:

1108

AN:

152284

Hom.:

Cov.:

AF XY:

0.00740

AC XY:

551

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.00161

Gnomad4 AMR

AF:

0.00131

Gnomad4 ASJ

AF:

0.00317

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.00228

Gnomad4 FIN

AF:

0.0188

Gnomad4 NFE

AF:

0.0117

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00911

Hom.:

Bravo

AF:

0.00555

TwinsUK

AF:

0.00782

AC:

ALSPAC

AF:

0.00986

AC:

ESP6500AA

AF:

0.00272

AC:

ESP6500EA

AF:

0.00907

AC:

ExAC

AF:

0.00727

AC:

883

Asia WGS

AF:

0.00173

AC:

AN:

3478

EpiCase

AF:

0.0101

EpiControl

AF:

0.00842

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	Apr 16, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.43

BayesDel_noAF

Benign

-0.37

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.037

Eigen

Benign

0.17

Eigen_PC

Uncertain

0.37

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Uncertain

0.92

MetaRNN

Benign

0.0077

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.0

PrimateAI

Uncertain

0.73

PROVEAN

Benign

-0.75

REVEL

Benign

0.14

Sift

Benign

0.35

Sift4G

Benign

0.40

Polyphen

0.22

Vest4

0.53

MVP

0.12

MPC

0.39

ClinPred

0.016

GERP RS

5.6

Varity_R

0.13

gMVP

0.27

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