chr22-37759490-A-G

Position:

• chr22-37759490-A-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000407319.7(TRIOBP):​c.1259A>G​(p.Lys420Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0193 in 1,603,498 control chromosomes in the GnomAD database, including 4,560 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.096 (2412 hom., cov: 33)
  • Exomes 𝑓: 0.011 (2148 hom.)
• Consequence: TRIOBP ENST00000407319.7 missense
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 2.39

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]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0043314397).
• BP6: Variant 22-37759490-A-G is Benign according to our data. Variant chr22-37759490-A-G is described in ClinVar as [Benign]. Clinvar id is 47853.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIOBP	NM_001039141.3	c.6324+226A>G		intron_variant		ENST00000644935.1
TRIOBP	NM_138632.2	c.1259A>G	p.Lys420Arg	missense_variant	8/8
TRIOBP	NM_007032.5	c.1185+226A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIOBP	ENST00000407319.7	c.1259A>G	p.Lys420Arg	missense_variant	8/8	1
TRIOBP	ENST00000644935.1	c.6324+226A>G		intron_variant			NM_001039141.3	A2
TRIOBP	ENST00000403663.6	c.1185+226A>G		intron_variant		1		P2
TRIOBP	ENST00000344404.10	c.*5807+226A>G		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0960 AC: 14599 AN: 152054 Hom.: 2405 Cov.: 33

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0357

Gnomad ASJ AF: 0.00692

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00276

Gnomad OTH AF: 0.0737

GnomAD3 exomes AF: 0.0274 AC: 6756 AN: 246744 Hom.: 1019 AF XY: 0.0206 AC XY: 2757 AN XY: 133822

Gnomad AFR exome AF: 0.344

Gnomad AMR exome AF: 0.0182

Gnomad ASJ exome AF: 0.00786

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000686

Gnomad FIN exome AF: 0.0000507

Gnomad NFE exome AF: 0.00309

Gnomad OTH exome AF: 0.0153

GnomAD4 exome AF: 0.0113 AC: 16355 AN: 1451326 Hom.: 2148 Cov.: 29 AF XY: 0.00991 AC XY: 7160 AN XY: 722652

Gnomad4 AFR exome AF: 0.344

Gnomad4 AMR exome AF: 0.0204

Gnomad4 ASJ exome AF: 0.00859

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000860

Gnomad4 FIN exome AF: 0.0000195

Gnomad4 NFE exome AF: 0.00196

Gnomad4 OTH exome AF: 0.0231

GnomAD4 genome AF: 0.0962 AC: 14636 AN: 152172 Hom.: 2412 Cov.: 33 AF XY: 0.0932 AC XY: 6936 AN XY: 74416

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.0356

Gnomad4 ASJ AF: 0.00692

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00124

Gnomad4 FIN AF: 0.0000942

Gnomad4 NFE AF: 0.00278

Gnomad4 OTH AF: 0.0729

Alfa AF: 0.0312 Hom.: 218

Bravo AF: 0.109

TwinsUK AF: 0.00135 AC: 5

ALSPAC AF: 0.00156 AC: 6

ESP6500AA AF: 0.324 AC: 1426

ESP6500EA AF: 0.00279 AC: 24

ExAC AF: 0.0327 AC: 3968

Asia WGS AF: 0.0180 AC: 63 AN: 3478

EpiCase AF: 0.00316

EpiControl AF: 0.00516

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 29, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	May 24, 2018	- -

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

May 07, 2012

Lys420Arg in Exon 17A of TRIOBP: This variant is not expected to have clinical s ignificance because it has been identified in 32.4% (1210/3738) of African Ameri can chromosomes from a broad population by the NHLBI Exome Sequencing Project (h ttp://evs.gs.washington.edu/EVS; dbSNP rs57799594). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.73	T
BayesDel_noAF	Benign	-0.68
CADD	Benign	18
DANN	Benign	0.64
Eigen	Benign	-0.58
Eigen_PC	Benign	-0.46
FATHMM_MKL	Benign	0.50	N
LIST_S2	Benign	0.28	.;T
MetaRNN	Benign	0.0043	T;T
MetaSVM	Benign	-0.96	T
MutationTaster	Benign	1.0	P;P;P
PROVEAN	Benign	0.99	N;.
REVEL	Benign	0.051
Sift	Uncertain	0.017	D;.
Sift4G	Benign	0.31	T;.
Vest4		0.11
ClinPred		0.013	T
GERP RS		2.9

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs57799594; hg19: chr22-38155497;