2-46480487-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001424184.1(TMEM247):c.200C>T(p.Pro67Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000355 in 1,551,546 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001424184.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM247 | NM_001424184.1 | c.200C>T | p.Pro67Leu | missense_variant | Exon 2 of 3 | NP_001411113.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM247 | ENST00000434431.2 | c.200C>T | p.Pro67Leu | missense_variant | Exon 2 of 3 | 5 | ENSP00000388684.1 | |||
ENSG00000284608 | ENST00000432241.5 | n.365-3757C>T | intron_variant | Intron 4 of 4 | 3 | |||||
ENSG00000253515 | ENST00000517716.2 | n.80-19244C>T | intron_variant | Intron 2 of 3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000256 AC: 39AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000358 AC: 56AN: 156362Hom.: 0 AF XY: 0.000241 AC XY: 20AN XY: 82896
GnomAD4 exome AF: 0.000366 AC: 512AN: 1399384Hom.: 0 Cov.: 32 AF XY: 0.000329 AC XY: 227AN XY: 690194
GnomAD4 genome AF: 0.000256 AC: 39AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.000310 AC XY: 23AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.200C>T (p.P67L) alteration is located in exon 2 (coding exon 2) of the TMEM247 gene. This alteration results from a C to T substitution at nucleotide position 200, causing the proline (P) at amino acid position 67 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at