2-227366135-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_024795.4(TM4SF20):c.359G>C(p.Ser120Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,613,822 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024795.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TM4SF20 | NM_024795.4 | c.359G>C | p.Ser120Thr | missense_variant | 3/4 | ENST00000304568.4 | |
TM4SF20 | XM_011511876.3 | c.158G>C | p.Ser53Thr | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TM4SF20 | ENST00000304568.4 | c.359G>C | p.Ser120Thr | missense_variant | 3/4 | 1 | NM_024795.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250954Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135666
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461564Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727070
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152258Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74450
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2021 | The c.359G>C (p.S120T) alteration is located in exon 3 (coding exon 3) of the TM4SF20 gene. This alteration results from a G to C substitution at nucleotide position 359, causing the serine (S) at amino acid position 120 to be replaced by a threonine (T). 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