14-90578192-G-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001010854.2(TTC7B):c.2224C>A(p.Leu742Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00644 in 1,614,154 control chromosomes in the GnomAD database, including 37 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0043 ( 2 hom., cov: 33)
Exomes 𝑓: 0.0067 ( 35 hom. )
Consequence
TTC7B
NM_001010854.2 missense
NM_001010854.2 missense
Scores
1
4
14
Clinical Significance
Conservation
PhyloP100: 8.10
Genes affected
TTC7B (HGNC:19858): (tetratricopeptide repeat domain 7B) Involved in phosphatidylinositol phosphate biosynthetic process and protein localization to plasma membrane. Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.009799242).
BP6
?
Variant 14-90578192-G-T is Benign according to our data. Variant chr14-90578192-G-T is described in ClinVar as [Benign]. Clinvar id is 773559.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 2 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC7B | NM_001010854.2 | c.2224C>A | p.Leu742Ile | missense_variant | 19/20 | ENST00000328459.11 | |
TTC7B | NM_001401365.1 | c.2437C>A | p.Leu813Ile | missense_variant | 21/22 | ||
TTC7B | NM_001320421.2 | c.1969C>A | p.Leu657Ile | missense_variant | 20/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC7B | ENST00000328459.11 | c.2224C>A | p.Leu742Ile | missense_variant | 19/20 | 1 | NM_001010854.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00426 AC: 649AN: 152264Hom.: 2 Cov.: 33
GnomAD3 genomes
?
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649
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33
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GnomAD3 exomes AF: 0.00405 AC: 1015AN: 250748Hom.: 4 AF XY: 0.00405 AC XY: 549AN XY: 135644
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GnomAD4 exome AF: 0.00667 AC: 9750AN: 1461772Hom.: 35 Cov.: 32 AF XY: 0.00638 AC XY: 4641AN XY: 727168
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GnomAD4 genome ? AF: 0.00426 AC: 649AN: 152382Hom.: 2 Cov.: 33 AF XY: 0.00401 AC XY: 299AN XY: 74520
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ESP6500AA
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ExAC
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485
Asia WGS
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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 submitter | clinical testing | Invitae | Dec 13, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Benign
DEOGEN2
Benign
T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
D;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at