GeneBe

rs547201931

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate

The NM_022173.4(TIA1):​c.764+10G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

TIA1
NM_022173.4 intron

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.69

Publications

0 publications found
Variant links:
Genes affected
TIA1 (HGNC:11802): (TIA1 cytotoxic granule associated RNA binding protein) The product encoded by this gene is a member of a RNA-binding protein family and possesses nucleolytic activity against cytotoxic lymphocyte (CTL) target cells. It has been suggested that this protein may be involved in the induction of apoptosis as it preferentially recognizes poly(A) homopolymers and induces DNA fragmentation in CTL targets. The major granule-associated species is a 15-kDa protein that is thought to be derived from the carboxyl terminus of the 40-kDa product by proteolytic processing. Alternative splicing resulting in different isoforms has been found for this gene. [provided by RefSeq, May 2017]
C2orf42 (HGNC:26056): (chromosome 2 open reading frame 42) Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 2-70216198-C-A is Benign according to our data. Variant chr2-70216198-C-A is described in ClinVar as Likely_benign. ClinVar VariationId is 1944919.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TIA1NM_022173.4 linkc.764+10G>T intron_variant Intron 10 of 12 ENST00000433529.7 NP_071505.2 P31483-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TIA1ENST00000433529.7 linkc.764+10G>T intron_variant Intron 10 of 12 2 NM_022173.4 ENSP00000401371.2 P31483-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1385698
Hom.:
0
Cov.:
28
AF XY:
0.00
AC XY:
0
AN XY:
688874
African (AFR)
AF:
0.00
AC:
0
AN:
28374
American (AMR)
AF:
0.00
AC:
0
AN:
27416
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
24080
East Asian (EAS)
AF:
0.00
AC:
0
AN:
35984
South Asian (SAS)
AF:
0.00
AC:
0
AN:
72906
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
52780
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5334
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1081460
Other (OTH)
AF:
0.00
AC:
0
AN:
57364
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
0
Bravo
AF:
0.00000378

ClinVar

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

Submissions by phenotype

Welander distal myopathy Benign:1
Jun 24, 2022
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.096
DANN
Benign
0.68
PhyloP100
-2.7
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0

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

Other links and lift over

dbSNP: rs547201931; hg19: chr2-70443330; API