chr3-149474911-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004617.4(TM4SF4):c.34G>A(p.Gly12Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000371 in 1,613,884 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 (★).
Frequency
Consequence
NM_004617.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TM4SF4 | NM_004617.4 | c.34G>A | p.Gly12Arg | missense_variant | 1/5 | ENST00000305354.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TM4SF4 | ENST00000305354.5 | c.34G>A | p.Gly12Arg | missense_variant | 1/5 | 1 | NM_004617.4 | P1 | |
TM4SF4 | ENST00000465758.1 | c.34G>A | p.Gly12Arg | missense_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000210 AC: 32AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000209 AC: 52AN: 249056Hom.: 0 AF XY: 0.000215 AC XY: 29AN XY: 135130
GnomAD4 exome AF: 0.000387 AC: 566AN: 1461578Hom.: 0 Cov.: 37 AF XY: 0.000362 AC XY: 263AN XY: 727084
GnomAD4 genome ? AF: 0.000210 AC: 32AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74474
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 15, 2023 | The c.34G>A (p.G12R) alteration is located in exon 1 (coding exon 1) of the TM4SF4 gene. This alteration results from a G to A substitution at nucleotide position 34, causing the glycine (G) at amino acid position 12 to be replaced by an arginine (R). 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