chr13-113801789-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_182614.4(TMEM255B):c.646G>A(p.Val216Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 1,610,744 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_182614.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM255B | NM_182614.4 | c.646G>A | p.Val216Ile | missense_variant | 7/9 | ENST00000375353.5 | |
TMEM255B | NM_001348663.2 | c.646G>A | p.Val216Ile | missense_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM255B | ENST00000375353.5 | c.646G>A | p.Val216Ile | missense_variant | 7/9 | 1 | NM_182614.4 | P1 | |
TMEM255B | ENST00000498692.1 | n.360G>A | non_coding_transcript_exon_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000371 AC: 9AN: 242624Hom.: 0 AF XY: 0.0000228 AC XY: 3AN XY: 131696
GnomAD4 exome AF: 0.0000199 AC: 29AN: 1458554Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 725338
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152190Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 10, 2023 | The c.646G>A (p.V216I) alteration is located in exon 7 (coding exon 7) of the TMEM255B gene. This alteration results from a G to A substitution at nucleotide position 646, causing the valine (V) at amino acid position 216 to be replaced by an isoleucine (I). 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