2-227363807-CCTCCAGAAT-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM4BS2
The NM_024795.4(TM4SF20):c.598_606delATTCTGGAG(p.Ile200_Glu202del) variant causes a conservative inframe deletion change. The variant allele was found at a frequency of 0.0000118 in 1,614,140 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024795.4 conservative_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TM4SF20 | NM_024795.4 | c.598_606delATTCTGGAG | p.Ile200_Glu202del | conservative_inframe_deletion | Exon 4 of 4 | ENST00000304568.4 | NP_079071.2 | |
TM4SF20 | XM_011511876.3 | c.397_405delATTCTGGAG | p.Ile133_Glu135del | conservative_inframe_deletion | Exon 5 of 5 | XP_011510178.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251484Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135916
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461886Hom.: 0 AF XY: 0.0000124 AC XY: 9AN XY: 727242
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152254Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74438
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant, c.598_606del, results in the deletion of 3 amino acid(s) of the TM4SF20 protein (p.Ile200_Glu202del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs749661328, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with TM4SF20-related conditions. ClinVar contains an entry for this variant (Variation ID: 1349656). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at