7-73865260-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_182504.4(TMEM270):c.340C>T(p.Leu114Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,442 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_182504.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM270 | NM_182504.4 | c.340C>T | p.Leu114Phe | missense_variant | Exon 2 of 3 | ENST00000320531.3 | NP_872310.2 | |
TMEM270 | XM_011515785.3 | c.49C>T | p.Leu17Phe | missense_variant | Exon 2 of 3 | XP_011514087.1 | ||
TMEM270 | XM_017011741.2 | c.49C>T | p.Leu17Phe | missense_variant | Exon 2 of 3 | XP_016867230.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM270 | ENST00000320531.3 | c.340C>T | p.Leu114Phe | missense_variant | Exon 2 of 3 | 1 | NM_182504.4 | ENSP00000316775.2 | ||
TMEM270 | ENST00000426490.1 | n.*280C>T | non_coding_transcript_exon_variant | Exon 3 of 4 | 5 | ENSP00000403621.1 | ||||
TMEM270 | ENST00000426490.1 | n.*280C>T | 3_prime_UTR_variant | Exon 3 of 4 | 5 | ENSP00000403621.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152238Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000804 AC: 2AN: 248778Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135038
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461204Hom.: 0 Cov.: 68 AF XY: 0.00000550 AC XY: 4AN XY: 726908
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152238Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.340C>T (p.L114F) alteration is located in exon 2 (coding exon 2) of the WBSCR28 gene. This alteration results from a C to T substitution at nucleotide position 340, causing the leucine (L) at amino acid position 114 to be replaced by a phenylalanine (F). 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