chr14-61280814-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001017970.3(TMEM30B):āc.334T>Gā(p.Tyr112Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,564,600 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 11/19 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y112H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001017970.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM30B | NM_001017970.3 | c.334T>G | p.Tyr112Asp | missense_variant | 1/1 | ENST00000555868.2 | |
PRKCH | XM_024449661.2 | c.-121+93146A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM30B | ENST00000555868.2 | c.334T>G | p.Tyr112Asp | missense_variant | 1/1 | NM_001017970.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000105 AC: 2AN: 190258Hom.: 0 AF XY: 0.0000192 AC XY: 2AN XY: 104060
GnomAD4 exome AF: 0.0000198 AC: 28AN: 1412474Hom.: 0 Cov.: 29 AF XY: 0.0000229 AC XY: 16AN XY: 699666
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 12, 2024 | The c.334T>G (p.Y112D) alteration is located in exon 1 (coding exon 1) of the TMEM30B gene. This alteration results from a T to G substitution at nucleotide position 334, causing the tyrosine (Y) at amino acid position 112 to be replaced by an aspartic acid (D). 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