rs190914241
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_001173990.3(TMEM216):c.220C>T(p.Leu74=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000929 in 1,613,904 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. LF74L?) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001173990.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM216 | NM_001173990.3 | c.220C>T | p.Leu74= | synonymous_variant | 3/5 | ENST00000515837.7 | |
TMEM216 | NM_001173991.3 | c.220C>T | p.Leu74= | synonymous_variant | 3/5 | ||
TMEM216 | NM_016499.6 | c.37C>T | p.Leu13= | synonymous_variant | 3/5 | ||
TMEM216 | NM_001330285.2 | c.37C>T | p.Leu13= | synonymous_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM216 | ENST00000515837.7 | c.220C>T | p.Leu74= | synonymous_variant | 3/5 | 2 | NM_001173990.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000441 AC: 11AN: 249234Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135214
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461626Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 727098
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152278Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74452
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Familial aplasia of the vermis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 14, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at