rs144304124
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_020458.4(TTC7A):āc.870C>Gā(p.Val290=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000912 in 1,613,574 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0051 ( 9 hom., cov: 32)
Exomes š: 0.00048 ( 7 hom. )
Consequence
TTC7A
NM_020458.4 synonymous
NM_020458.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.00600
Genes affected
TTC7A (HGNC:19750): (tetratricopeptide repeat domain 7A) This gene encodes a protein containing tetratricopeptide repeats. Mutations in this gene disrupt intestinal development and can cause early onset inflammatory bowel disease and intestinal atresia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
?
Variant 2-46994383-C-G is Benign according to our data. Variant chr2-46994383-C-G is described in ClinVar as [Benign]. Clinvar id is 458803.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-46994383-C-G is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-0.006 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00505 (769/152258) while in subpopulation AFR AF= 0.0173 (718/41540). AF 95% confidence interval is 0.0162. There are 9 homozygotes in gnomad4. There are 350 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC7A | NM_020458.4 | c.870C>G | p.Val290= | synonymous_variant | 7/20 | ENST00000319190.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC7A | ENST00000319190.11 | c.870C>G | p.Val290= | synonymous_variant | 7/20 | 2 | NM_020458.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00505 AC: 769AN: 152140Hom.: 9 Cov.: 32
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GnomAD3 exomes AF: 0.00135 AC: 338AN: 249944Hom.: 4 AF XY: 0.000984 AC XY: 133AN XY: 135202
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GnomAD4 exome AF: 0.000480 AC: 702AN: 1461316Hom.: 7 Cov.: 31 AF XY: 0.000428 AC XY: 311AN XY: 726956
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GnomAD4 genome ? AF: 0.00505 AC: 769AN: 152258Hom.: 9 Cov.: 32 AF XY: 0.00470 AC XY: 350AN XY: 74432
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Multiple gastrointestinal atresias Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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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