chr19-47046085-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017854.2(TMEM160):āc.469A>Gā(p.Met157Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000389 in 1,542,620 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_017854.2 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 |
---|---|---|---|---|---|---|---|
TMEM160 | NM_017854.2 | c.469A>G | p.Met157Val | missense_variant | 3/3 | ENST00000253047.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM160 | ENST00000253047.7 | c.469A>G | p.Met157Val | missense_variant | 3/3 | 1 | NM_017854.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151982Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000215 AC: 3AN: 139570Hom.: 0 AF XY: 0.0000130 AC XY: 1AN XY: 76952
GnomAD4 exome AF: 0.0000410 AC: 57AN: 1390526Hom.: 0 Cov.: 32 AF XY: 0.0000364 AC XY: 25AN XY: 687506
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152094Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 23, 2023 | The c.469A>G (p.M157V) alteration is located in exon 3 (coding exon 3) of the TMEM160 gene. This alteration results from a A to G substitution at nucleotide position 469, causing the methionine (M) at amino acid position 157 to be replaced by a valine (V). 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