chr6-44275841-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001137560.2(TMEM151B):c.1015G>A(p.Gly339Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00011 in 1,542,032 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G339V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001137560.2 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 |
---|---|---|---|---|---|---|---|
TMEM151B | NM_001137560.2 | c.1015G>A | p.Gly339Ser | missense_variant | 3/3 | ENST00000451188.7 | |
POLR1C | NM_001318876.2 | c.946-166049G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM151B | ENST00000451188.7 | c.1015G>A | p.Gly339Ser | missense_variant | 3/3 | 5 | NM_001137560.2 | P1 | |
TMEM151B | ENST00000438774.2 | c.576+2335G>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000585 AC: 89AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000122 AC: 17AN: 139672Hom.: 0 AF XY: 0.0000396 AC XY: 3AN XY: 75718
GnomAD4 exome AF: 0.0000576 AC: 80AN: 1389716Hom.: 0 Cov.: 33 AF XY: 0.0000525 AC XY: 36AN XY: 685576
GnomAD4 genome ? AF: 0.000584 AC: 89AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.000403 AC XY: 30AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 18, 2023 | The c.1015G>A (p.G339S) alteration is located in exon 3 (coding exon 3) of the TMEM151B gene. This alteration results from a G to A substitution at nucleotide position 1015, causing the glycine (G) at amino acid position 339 to be replaced by a serine (S). 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