6-166160974-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001366285.2(TBXT):​c.908-8C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00562 in 1,613,648 control chromosomes in the GnomAD database, including 429 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.030 ( 230 hom., cov: 33)
Exomes 𝑓: 0.0030 ( 199 hom. )

Consequence

TBXT
NM_001366285.2 splice_region, splice_polypyrimidine_tract, intron

Scores

2
Splicing: ADA: 0.00002854
2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.409
Variant links:
Genes affected
TBXT (HGNC:11515): (T-box transcription factor T) The protein encoded by this gene is an embryonic nuclear transcription factor that binds to a specific DNA element, the palindromic T-site. It binds through a region in its N-terminus, called the T-box, and effects transcription of genes required for mesoderm formation and differentiation. The protein is localized to notochord-derived cells. Variation in this gene was associated with susceptibility to neural tube defects and chordoma. A mutation in this gene was found in a family with sacral agenesis with vertebral anomalies. [provided by RefSeq, Sep 2018]

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 (BayesDel_noAF=-0.93).
BP6
Variant 6-166160974-G-A is Benign according to our data. Variant chr6-166160974-G-A is described in ClinVar as [Benign]. Clinvar id is 768118.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TBXTNM_001366285.2 linkuse as main transcriptc.908-8C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant ENST00000366876.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TBXTENST00000366876.7 linkuse as main transcriptc.908-8C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 1 NM_001366285.2 P4
TBXTENST00000366871.7 linkuse as main transcriptc.731-8C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 1 O15178-2
TBXTENST00000296946.6 linkuse as main transcriptc.905-8C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 5 A1O15178-1

Frequencies

GnomAD3 genomes
AF:
0.0303
AC:
4615
AN:
152142
Hom.:
230
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.107
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00956
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.000176
Gnomad OTH
AF:
0.0186
GnomAD3 exomes
AF:
0.00768
AC:
1930
AN:
251202
Hom.:
90
AF XY:
0.00557
AC XY:
756
AN XY:
135738
show subpopulations
Gnomad AFR exome
AF:
0.108
Gnomad AMR exome
AF:
0.00402
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.000131
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000114
Gnomad OTH exome
AF:
0.00375
GnomAD4 exome
AF:
0.00305
AC:
4451
AN:
1461388
Hom.:
199
Cov.:
33
AF XY:
0.00260
AC XY:
1888
AN XY:
726970
show subpopulations
Gnomad4 AFR exome
AF:
0.110
Gnomad4 AMR exome
AF:
0.00497
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.000232
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000827
Gnomad4 OTH exome
AF:
0.00654
GnomAD4 genome
AF:
0.0303
AC:
4616
AN:
152260
Hom.:
230
Cov.:
33
AF XY:
0.0290
AC XY:
2162
AN XY:
74442
show subpopulations
Gnomad4 AFR
AF:
0.106
Gnomad4 AMR
AF:
0.00954
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000176
Gnomad4 OTH
AF:
0.0184
Alfa
AF:
0.0158
Hom.:
45
Bravo
AF:
0.0340
Asia WGS
AF:
0.00404
AC:
15
AN:
3478

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.30
DANN
Benign
0.20

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.000029
dbscSNV1_RF
Benign
0.0
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: rs61597882; hg19: chr6-166574462; API