19-16680108-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_024074.4(TMEM38A):c.249C>G(p.Asn83Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000379 in 1,610,212 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024074.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM38A | ENST00000187762.7 | c.249C>G | p.Asn83Lys | missense_variant | Exon 2 of 6 | 1 | NM_024074.4 | ENSP00000187762.1 | ||
TMEM38A | ENST00000599479.1 | c.204C>G | p.Asn68Lys | missense_variant | Exon 2 of 4 | 3 | ENSP00000469721.1 | |||
TMEM38A | ENST00000595452.1 | n.225C>G | non_coding_transcript_exon_variant | Exon 2 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152250Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248146Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134418
GnomAD4 exome AF: 0.0000405 AC: 59AN: 1457962Hom.: 0 Cov.: 31 AF XY: 0.0000386 AC XY: 28AN XY: 725486
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152250Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.249C>G (p.N83K) alteration is located in exon 2 (coding exon 2) of the TMEM38A gene. This alteration results from a C to G substitution at nucleotide position 249, causing the asparagine (N) at amino acid position 83 to be replaced by a lysine (K). 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