rs138139146

Positions:

chr22-37769262-G-A

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2

The NM_001039141.3(TRIOBP):c.6736G>A(p.Glu2246Lys) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00695 in 1,609,952 control chromosomes in the GnomAD database, including 52 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0047 ( 5 hom., cov: 32)

Exomes 𝑓: 0.0072 ( 47 hom. )

Consequence

TRIOBP
NM_001039141.3 missense, splice_region

Scores

Splicing: ADA: 0.9994

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 5.65

Variant links:

Genes affected

TRIOBP (HGNC:17009): (TRIO and F-actin binding protein) This gene encodes a protein with an N-terminal pleckstrin homology domain and a C-terminal coiled-coil region. The protein interacts with trio, which is involved with neural tissue development and controlling actin cytoskeleton organization, cell motility and cell growth. The protein also associates with F-actin and stabilizes F-actin structures. Mutations in this gene have been associated with a form of autosomal recessive nonsyndromic deafness. Multiple alternatively spliced transcript variants that would encode different isoforms have been found for this gene, however some transcripts may be subject to nonsense-mediated decay (NMD). [provided by RefSeq, Nov 2008]

TRIOBP links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 22-37769262-G-A is Benign according to our data. Variant chr22-37769262-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 165614.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00472 (719/152374) while in subpopulation NFE AF= 0.007 (476/68028). AF 95% confidence interval is 0.00648. There are 5 homozygotes in gnomad4. There are 344 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIOBP	NM_001039141.3 linkuse as main transcript	c.6736G>A	p.Glu2246Lys	missense_variant, splice_region_variant	21/24	ENST00000644935.1	NP_001034230.1	Q9H2D6-1
TRIOBP	NM_007032.5 linkuse as main transcript	c.1597G>A	p.Glu533Lys	missense_variant, splice_region_variant	11/14		NP_008963.3	Q9H2D6-7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TRIOBP	ENST00000644935.1 linkuse as main transcript	c.6736G>A	p.Glu2246Lys	missense_variant, splice_region_variant	21/24		NM_001039141.3	ENSP00000496394.1	Q9H2D6-1
TRIOBP	ENST00000403663.6 linkuse as main transcript	c.1597G>A	p.Glu533Lys	missense_variant, splice_region_variant	11/14	1		ENSP00000386026.2	Q9H2D6-7
TRIOBP	ENST00000344404.10 linkuse as main transcript	n.*6219G>A		splice_region_variant, non_coding_transcript_exon_variant	19/22	2		ENSP00000340312.6	H7BXW4
TRIOBP	ENST00000344404.10 linkuse as main transcript	n.*6219G>A		3_prime_UTR_variant	19/22	2		ENSP00000340312.6	H7BXW4

Frequencies

GnomAD3 genomes

AF:

0.00472

AC:

719

AN:

152256

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00162

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00530

Gnomad ASJ

AF:

0.0170

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.00179

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00700

Gnomad OTH

AF:

0.00573

GnomAD3 exomes

AF:

0.00532

AC:

1273

AN:

239260

Hom.:

AF XY:

0.00526

AC XY:

688

AN XY:

130708

show subpopulations

Gnomad AFR exome

AF:

0.00138

Gnomad AMR exome

AF:

0.00492

Gnomad ASJ exome

AF:

0.0150

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000873

Gnomad FIN exome

AF:

0.00214

Gnomad NFE exome

AF:

0.00765

Gnomad OTH exome

AF:

0.00770

GnomAD4 exome

AF:

0.00719

AC:

10478

AN:

1457578

Hom.:

Cov.:

AF XY:

0.00699

AC XY:

5067

AN XY:

724886

show subpopulations

Gnomad4 AFR exome

AF:

0.00141

Gnomad4 AMR exome

AF:

0.00545

Gnomad4 ASJ exome

AF:

0.0162

Gnomad4 EAS exome

AF:

0.0000254

Gnomad4 SAS exome

AF:

0.000981

Gnomad4 FIN exome

AF:

0.00171

Gnomad4 NFE exome

AF:

0.00820

Gnomad4 OTH exome

AF:

0.00733

GnomAD4 genome

AF:

0.00472

AC:

719

AN:

152374

Hom.:

Cov.:

AF XY:

0.00462

AC XY:

344

AN XY:

74510

show subpopulations

Gnomad4 AFR

AF:

0.00161

Gnomad4 AMR

AF:

0.00529

Gnomad4 ASJ

AF:

0.0170

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000621

Gnomad4 FIN

AF:

0.00179

Gnomad4 NFE

AF:

0.00700

Gnomad4 OTH

AF:

0.00567

Alfa

AF:

0.00715

Hom.:

Bravo

AF:

0.00524

TwinsUK

AF:

0.00998

AC:

ALSPAC

AF:

0.00908

AC:

ESP6500AA

AF:

0.00173

AC:

ESP6500EA

AF:

0.00564

AC:

ExAC

AF:

0.00490

AC:

592

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Apr 30, 2012	Glu2246Lys in Exon 21 of TRIOBP: This variant is not expected to have clinical s ignificance because it has been identified in 0.5% (37/6742) of European America n chromosomes from a broad population by the NHLBI Exome Sequencing Project (htt p://evs.gs.washington.edu/EVS; dbSNP rs138139146). -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Feb 09, 2015	- -
Likely benign, criteria provided, single submitter	clinical testing	Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	Jul 17, 2015	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

not provided

Benign:4

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 25, 2024	- -
Likely benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Feb 18, 2019	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 28, 2018	This variant is associated with the following publications: (PMID: 26969326, 28089734, 29197352) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.38

BayesDel_addAF

Benign

-0.37

BayesDel_noAF

Benign

-0.30

CADD

Pathogenic

DANN

Pathogenic

1.0

DEOGEN2

Benign

0.36

T;T;.

Eigen

Uncertain

0.65

Eigen_PC

Uncertain

0.60

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Uncertain

0.93

.;D;D

M_CAP

Uncertain

0.11

MetaRNN

Benign

0.0071

T;T;T

MetaSVM

Benign

-0.85

MutationAssessor

Uncertain

2.5

M;M;.

PrimateAI

Uncertain

0.56

PROVEAN

Uncertain

-3.3

D;.;D

REVEL

Benign

0.15

Sift

Uncertain

0.0020

D;.;D

Sift4G

Uncertain

0.0050

D;.;D

Polyphen

1.0

D;D;.

Vest4

0.84

MVP

0.55

MPC

0.58

ClinPred

0.017

GERP RS

4.4

Varity_R

0.37

gMVP

0.20

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Pathogenic

1.0

dbscSNV1_RF

Pathogenic

0.92

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