2-165941072-T-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_024753.5(TTC21B):c.665A>T(p.Gln222Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00216 in 1,613,962 control chromosomes in the GnomAD database, including 80 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_024753.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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TTC21B | NM_024753.5 | c.665A>T | p.Gln222Leu | missense_variant | Exon 6 of 29 | ENST00000243344.8 | NP_079029.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0119 AC: 1817AN: 152182Hom.: 39 Cov.: 33
GnomAD3 exomes AF: 0.00299 AC: 752AN: 251252Hom.: 18 AF XY: 0.00207 AC XY: 281AN XY: 135786
GnomAD4 exome AF: 0.00114 AC: 1661AN: 1461662Hom.: 41 Cov.: 32 AF XY: 0.000959 AC XY: 697AN XY: 727138
GnomAD4 genome AF: 0.0119 AC: 1819AN: 152300Hom.: 39 Cov.: 33 AF XY: 0.0112 AC XY: 832AN XY: 74480
ClinVar
Submissions by phenotype
not specified Benign:5
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. -
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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. -
not provided Benign:4
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TTC21B: BP4, BS1, BS2 -
Asphyxiating thoracic dystrophy 4;C3151186:Nephronophthisis 12 Benign:1
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Asphyxiating thoracic dystrophy 4 Benign:1
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 allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Jeune thoracic dystrophy;C0687120:Nephronophthisis Benign:1
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Nephronophthisis 12 Benign:1
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). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Connective tissue disorder Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at