Y-7063916-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_033284.2(TBL1Y):​c.224G>T​(p.Ser75Ile) variant causes a missense change involving the alteration of a conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 10/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0015 ( 0 hom., 48 hem., cov: 0)
Exomes 𝑓: 0.0015 ( 0 hom. 556 hem. )

Consequence

TBL1Y
NM_033284.2 missense

Scores

2
11

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 8.39
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.008928269).
BP6
Variant Y-7063916-G-T is Benign according to our data. Variant chrY-7063916-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 2661885.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00153 (556/362880) while in subpopulation MID AF= 0.0221 (36/1629). AF 95% confidence interval is 0.0164. There are 0 homozygotes in gnomad4_exome. There are 556 alleles in male gnomad4_exome subpopulation. Median coverage is 15. This position pass quality control queck.
BS2
High Hemizygotes in GnomAd4 at 48 YL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TBL1YNM_033284.2 linkc.224G>T p.Ser75Ile missense_variant Exon 8 of 19 ENST00000383032.6 NP_150600.1 Q9BQ87A0A024R189
TBL1YNM_134258.2 linkc.224G>T p.Ser75Ile missense_variant Exon 7 of 18 NP_599020.1 Q9BQ87A0A024R189
TBL1YNM_134259.2 linkc.224G>T p.Ser75Ile missense_variant Exon 7 of 18 NP_599021.1 Q9BQ87A0A024R189

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TBL1YENST00000383032.6 linkc.224G>T p.Ser75Ile missense_variant Exon 8 of 19 1 NM_033284.2 ENSP00000372499.1 Q9BQ87
TBL1YENST00000346432.3 linkc.224G>T p.Ser75Ile missense_variant Exon 7 of 18 1 ENSP00000328879.4 Q9BQ87
TBL1YENST00000355162.6 linkc.224G>T p.Ser75Ile missense_variant Exon 7 of 18 1 ENSP00000347289.2 Q9BQ87

Frequencies

GnomAD3 genomes
AF:
0.00146
AC:
48
AN:
32785
Hom.:
0
Cov.:
0
AF XY:
0.00146
AC XY:
48
AN XY:
32785
show subpopulations
Gnomad AFR
AF:
0.000360
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00335
Gnomad ASJ
AF:
0.0182
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000710
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00134
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00235
AC:
158
AN:
67143
Hom.:
0
AF XY:
0.00235
AC XY:
158
AN XY:
67143
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00503
Gnomad ASJ exome
AF:
0.0116
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000875
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00247
Gnomad OTH exome
AF:
0.00314
GnomAD4 exome
AF:
0.00153
AC:
556
AN:
362880
Hom.:
0
Cov.:
15
AF XY:
0.00153
AC XY:
556
AN XY:
362880
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00536
Gnomad4 ASJ exome
AF:
0.0110
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000881
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00116
Gnomad4 OTH exome
AF:
0.00386
GnomAD4 genome
AF:
0.00146
AC:
48
AN:
32850
Hom.:
0
Cov.:
0
AF XY:
0.00146
AC XY:
48
AN XY:
32850
show subpopulations
Gnomad4 AFR
AF:
0.000358
Gnomad4 AMR
AF:
0.00334
Gnomad4 ASJ
AF:
0.0182
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000707
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00134
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.00872
Hom.:
88
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.00214
AC:
4
ExAC
AF:
0.00208
AC:
149

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Oct 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

TBL1Y: BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.13
BayesDel_addAF
Benign
-0.58
T
BayesDel_noAF
Benign
-0.61
CADD
Uncertain
25
DANN
Benign
0.83
DEOGEN2
Benign
0.038
T;T;T
FATHMM_MKL
Uncertain
0.97
D
LIST_S2
Uncertain
0.86
.;.;D
MetaRNN
Benign
0.0089
T;T;T
MutationAssessor
Benign
0.90
L;L;L
PROVEAN
Benign
-1.0
N;N;N
Sift
Benign
0.15
T;T;T
Sift4G
Benign
0.46
T;T;T
Polyphen
0.044
B;B;B
Vest4
0.14
MVP
0.11
GERP RS
2.3
Varity_R
0.22
gMVP
0.92

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.

Other links and lift over

dbSNP: rs200332530; hg19: chrY-6931957; API