3-196327556-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_138461.4(TM4SF19):c.35G>A(p.Arg12Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000415 in 1,613,574 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R12W) has been classified as Uncertain significance.
Frequency
Consequence
NM_138461.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TM4SF19 | NM_138461.4 | c.35G>A | p.Arg12Gln | missense_variant | Exon 2 of 5 | ENST00000273695.4 | NP_612470.2 | |
TM4SF19 | NM_001204897.2 | c.35G>A | p.Arg12Gln | missense_variant | Exon 2 of 5 | NP_001191826.1 | ||
TM4SF19 | NM_001204898.2 | c.35G>A | p.Arg12Gln | missense_variant | Exon 2 of 4 | NP_001191827.1 | ||
TM4SF19-DYNLT2B | NR_037950.1 | n.193G>A | non_coding_transcript_exon_variant | Exon 2 of 6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TM4SF19 | ENST00000273695.4 | c.35G>A | p.Arg12Gln | missense_variant | Exon 2 of 5 | 1 | NM_138461.4 | ENSP00000273695.4 | ||
TM4SF19 | ENST00000446879.5 | c.35G>A | p.Arg12Gln | missense_variant | Exon 2 of 6 | 1 | ENSP00000395280.1 | |||
TM4SF19 | ENST00000454715.5 | c.35G>A | p.Arg12Gln | missense_variant | Exon 2 of 4 | 1 | ENSP00000387728.1 | |||
TM4SF19-DYNLT2B | ENST00000442633.1 | n.35G>A | non_coding_transcript_exon_variant | Exon 2 of 6 | 1 | ENSP00000405973.1 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152074Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251082Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135768
GnomAD4 exome AF: 0.0000328 AC: 48AN: 1461500Hom.: 0 Cov.: 31 AF XY: 0.0000358 AC XY: 26AN XY: 727054
GnomAD4 genome AF: 0.000125 AC: 19AN: 152074Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.35G>A (p.R12Q) alteration is located in exon 2 (coding exon 1) of the TM4SF19 gene. This alteration results from a G to A substitution at nucleotide position 35, causing the arginine (R) at amino acid position 12 to be replaced by a glutamine (Q). 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