2-119437168-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_183240.3(TMEM37):c.301G>T(p.Ala101Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000372 in 1,614,116 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_183240.3 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 |
---|---|---|---|---|---|---|---|
TMEM37 | NM_183240.3 | c.301G>T | p.Ala101Ser | missense_variant | 2/2 | ENST00000306406.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM37 | ENST00000306406.5 | c.301G>T | p.Ala101Ser | missense_variant | 2/2 | 1 | NM_183240.3 | P2 | |
TMEM37 | ENST00000409826.1 | c.337G>T | p.Ala113Ser | missense_variant | 2/2 | 3 | A2 | ||
TMEM37 | ENST00000465296.1 | n.441G>T | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000250 AC: 38AN: 152230Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000163 AC: 41AN: 251446Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135910
GnomAD4 exome AF: 0.000384 AC: 562AN: 1461886Hom.: 0 Cov.: 35 AF XY: 0.000396 AC XY: 288AN XY: 727248
GnomAD4 genome AF: 0.000250 AC: 38AN: 152230Hom.: 0 Cov.: 34 AF XY: 0.000202 AC XY: 15AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 10, 2023 | The c.301G>T (p.A101S) alteration is located in exon 2 (coding exon 2) of the TMEM37 gene. This alteration results from a G to T substitution at nucleotide position 301, causing the alanine (A) at amino acid position 101 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