chr10-7824594-T-A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_031923.4(TAF3):​c.409+34T>A 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 34)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

TAF3
NM_031923.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.415

Publications

9 publications found
Variant links:
Genes affected
TAF3 (HGNC:17303): (TATA-box binding protein associated factor 3) The highly conserved RNA polymerase II transcription factor TFIID (see TAF1; MIM 313650) comprises the TATA box-binding protein (TBP; MIM 600075) and a set of TBP-associated factors (TAFs), including TAF3. TAFs contribute to promoter recognition and selectivity and act as antiapoptotic factors (Gangloff et al., 2001 [PubMed 11438666]).[supplied by OMIM, May 2009]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TAF3NM_031923.4 linkc.409+34T>A intron_variant Intron 2 of 6 ENST00000344293.6 NP_114129.1 Q5VWG9
TAF3XM_011519741.2 linkc.409+34T>A intron_variant Intron 2 of 6 XP_011518043.2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TAF3ENST00000344293.6 linkc.409+34T>A intron_variant Intron 2 of 6 1 NM_031923.4 ENSP00000340271.5 Q5VWG9

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
1449774
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
719924
African (AFR)
AF:
0.00
AC:
0
AN:
33036
American (AMR)
AF:
0.00
AC:
0
AN:
43720
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25670
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39536
South Asian (SAS)
AF:
0.00
AC:
0
AN:
85290
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
52810
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5706
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1104108
Other (OTH)
AF:
0.00
AC:
0
AN:
59898
GnomAD4 genome
Cov.:
34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
4.5
DANN
Benign
0.71
PhyloP100
-0.41

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: rs1244471; hg19: chr10-7866557; API