chr6-158479880-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020245.5(TULP4):c.1156G>A(p.Ala386Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,461,170 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000068 ( 0 hom. )
Consequence
TULP4
NM_020245.5 missense
NM_020245.5 missense
Scores
2
5
12
Clinical Significance
Conservation
PhyloP100: 7.55
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TULP4 | NM_020245.5 | c.1156G>A | p.Ala386Thr | missense_variant | 7/14 | ENST00000367097.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TULP4 | ENST00000367097.8 | c.1156G>A | p.Ala386Thr | missense_variant | 7/14 | 1 | NM_020245.5 | P1 | |
TULP4 | ENST00000367094.6 | c.1156G>A | p.Ala386Thr | missense_variant | 7/13 | 1 | |||
TULP4 | ENST00000616856.1 | n.1728G>A | non_coding_transcript_exon_variant | 7/8 | 2 | ||||
TULP4 | ENST00000613390.1 | c.211G>A | p.Ala71Thr | missense_variant, NMD_transcript_variant | 2/6 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250660Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135570
GnomAD3 exomes
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2
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250660
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135570
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GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461170Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726924
GnomAD4 exome
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AN:
1461170
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31
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AN XY:
726924
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GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 12, 2023 | The c.1156G>A (p.A386T) alteration is located in exon 7 (coding exon 7) of the TULP4 gene. This alteration results from a G to A substitution at nucleotide position 1156, causing the alanine (A) at amino acid position 386 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Pathogenic
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationAssessor
Benign
L;L
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
D;T
Sift4G
Benign
T;T
Polyphen
D;D
Vest4
MutPred
Loss of sheet (P = 0.1158);Loss of sheet (P = 0.1158);
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at