chr2-165949632-G-C
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_024753.5(TTC21B):āc.114C>Gā(p.Val38=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00153 in 1,613,594 control chromosomes in the GnomAD database, including 37 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. V38V) has been classified as Likely benign.
Frequency
Consequence
NM_024753.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TTC21B | NM_024753.5 | c.114C>G | p.Val38= | synonymous_variant | 2/29 | ENST00000243344.8 | |
TTC21B | XM_017004967.2 | c.114C>G | p.Val38= | synonymous_variant | 2/28 | ||
TTC21B | XM_006712761.2 | c.114C>G | p.Val38= | synonymous_variant | 2/23 | ||
TTC21B | XM_011511872.3 | c.114C>G | p.Val38= | synonymous_variant | 2/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TTC21B | ENST00000243344.8 | c.114C>G | p.Val38= | synonymous_variant | 2/29 | 1 | NM_024753.5 | P1 | |
TTC21B-AS1 | ENST00000440322.5 | n.2001G>C | non_coding_transcript_exon_variant | 4/4 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00830 AC: 1263AN: 152114Hom.: 22 Cov.: 32
GnomAD3 exomes AF: 0.00196 AC: 490AN: 249670Hom.: 7 AF XY: 0.00155 AC XY: 209AN XY: 135118
GnomAD4 exome AF: 0.000820 AC: 1199AN: 1461362Hom.: 15 Cov.: 31 AF XY: 0.000710 AC XY: 516AN XY: 726974
GnomAD4 genome AF: 0.00831 AC: 1265AN: 152232Hom.: 22 Cov.: 32 AF XY: 0.00763 AC XY: 568AN XY: 74432
ClinVar
Submissions by phenotype
not specified Benign:3
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 06, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Jeune thoracic dystrophy;C0687120:Nephronophthisis Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Asphyxiating thoracic dystrophy 4 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Oct 16, 2023 | - - |
Nephronophthisis 12 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. - |
Connective tissue disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | May 01, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at