chr22-30612945-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_000355.4(TCN2):c.330C>T(p.Leu110=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00062 in 1,614,178 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. L110L) has been classified as Likely benign.
Frequency
Consequence
NM_000355.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TCN2 | NM_000355.4 | c.330C>T | p.Leu110= | synonymous_variant | 3/9 | ENST00000215838.8 | |
TCN2 | NM_001184726.2 | c.330C>T | p.Leu110= | synonymous_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCN2 | ENST00000215838.8 | c.330C>T | p.Leu110= | synonymous_variant | 3/9 | 1 | NM_000355.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000394 AC: 60AN: 152198Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00128 AC: 323AN: 251378Hom.: 5 AF XY: 0.00171 AC XY: 232AN XY: 135872
GnomAD4 exome AF: 0.000644 AC: 941AN: 1461862Hom.: 15 Cov.: 32 AF XY: 0.000924 AC XY: 672AN XY: 727232
GnomAD4 genome AF: 0.000394 AC: 60AN: 152316Hom.: 2 Cov.: 32 AF XY: 0.000537 AC XY: 40AN XY: 74480
ClinVar
Submissions by phenotype
Transcobalamin II deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at