Variant Y-7064105-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6BS2_Supporting

The ENST00000383032.6(TBL1Y):c.413G>A(p.Arg138Gln) variant causes a missense change. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.00033 ( 0 hom., 11 hem., cov: 0)

Exomes 𝑓: 0.00035 ( 0 hom. 127 hem. )

Consequence

TBL1Y
ENST00000383032.6 missense

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 5.32

Variant links:

Genes affected

TBL1Y (HGNC:18502): (transducin beta like 1 Y-linked) The protein encoded by this gene has sequence similarity with members of the WD40 repeat-containing protein family. The WD40 group is a large family of proteins, which appear to have a regulatory function. It is believed that the WD40 repeats mediate protein-protein interactions and members of the family are involved in signal transduction, RNA processing, gene regulation, vesicular trafficking, cytoskeletal assembly and may play a role in the control of cytotypic differentiation. This gene is highly similar to TBL1X gene in nucleotide sequence and protein sequence, but the TBL1X gene is located on chromosome X and this gene is on chromosome Y. This gene has three alternatively spliced transcript variants encoding the same protein. [provided by RefSeq, Jul 2008]

TBL1Y links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.014740616).

BP6

Variant Y-7064105-G-A is Benign according to our data. Variant chrY-7064105-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3033002.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High Hemizygotes in GnomAd4 at 11 YL geneVariant has number of hemizygotes lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
TBL1Y	NM_033284.2 linkuse as main transcript	c.413G>A	p.Arg138Gln	missense_variant	8/19	ENST00000383032.6	NP_150600.1
TBL1Y	NM_134258.2 linkuse as main transcript	c.413G>A	p.Arg138Gln	missense_variant	7/18		NP_599020.1
TBL1Y	NM_134259.2 linkuse as main transcript	c.413G>A	p.Arg138Gln	missense_variant	7/18		NP_599021.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
TBL1Y	ENST00000383032.6 linkuse as main transcript	c.413G>A	p.Arg138Gln	missense_variant	8/19	1	NM_033284.2	ENSP00000372499	P1
TBL1Y	ENST00000346432.3 linkuse as main transcript	c.413G>A	p.Arg138Gln	missense_variant	7/18	1		ENSP00000328879	P1
TBL1Y	ENST00000355162.6 linkuse as main transcript	c.413G>A	p.Arg138Gln	missense_variant	7/18	1		ENSP00000347289	P1

Frequencies

GnomAD3 genomes

AF:

0.000327

AC:

AN:

33676

Hom.:

Cov.:

AF XY:

0.000327

AC XY:

AN XY:

33676

show subpopulations

Gnomad AFR

AF:

0.000233

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000270

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00239

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000367

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000270

AC:

AN:

66764

Hom.:

AF XY:

0.000270

AC XY:

AN XY:

66764

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000665

Gnomad SAS exome

AF:

0.000438

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000324

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000350

AC:

127

AN:

362937

Hom.:

Cov.:

AF XY:

0.000350

AC XY:

127

AN XY:

362937

show subpopulations

Gnomad4 AFR exome

AF:

0.000141

Gnomad4 AMR exome

AF:

0.000105

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000633

Gnomad4 SAS exome

AF:

0.000535

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000326

Gnomad4 OTH exome

AF:

0.000771

GnomAD4 genome

AF:

0.000326

AC:

AN:

33740

Hom.:

Cov.:

AF XY:

0.000326

AC XY:

AN XY:

33740

show subpopulations

Gnomad4 AFR

AF:

0.000231

Gnomad4 AMR

AF:

0.000269

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00239

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000367

Gnomad4 OTH

AF:

0.00

ExAC

AF:

0.000259

AC:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

TBL1Y-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 04, 2023

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.066

BayesDel_addAF

Benign

-0.61

BayesDel_noAF

Benign

-0.75

CADD

Benign

DANN

Benign

0.71

DEOGEN2

Benign

0.031

T;T;T

FATHMM_MKL

Uncertain

0.94

LIST_S2

Benign

0.64

.;.;T

M_CAP

Benign

0.015

MetaRNN

Benign

0.015

T;T;T

MutationAssessor

Benign

0.69

N;N;N

MutationTaster

Benign

1.0

D;N;N;N

PROVEAN

Benign

0.45

N;N;N

Sift

Benign

0.63

T;T;T

Sift4G

Benign

0.72

T;T;T

Polyphen

0.091

B;B;B

Vest4

0.083

MVP

0.10

GERP RS

2.3

Varity_R

0.064

gMVP

0.40

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