rs10569304
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_025268.4(TMEM121):c.887_898del(p.Pro296_Pro299del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.0000209 in 1,527,674 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000023 ( 1 hom. )
Consequence
TMEM121
NM_025268.4 inframe_deletion
NM_025268.4 inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.00
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM121 | NM_025268.4 | c.887_898del | p.Pro296_Pro299del | inframe_deletion | 2/2 | ENST00000392519.7 | |
TMEM121 | NM_001331238.2 | c.887_898del | p.Pro296_Pro299del | inframe_deletion | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM121 | ENST00000392519.7 | c.887_898del | p.Pro296_Pro299del | inframe_deletion | 2/2 | 1 | NM_025268.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151668Hom.: 0 Cov.: 0
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GnomAD3 exomes AF: 0.0000925 AC: 11AN: 118980Hom.: 0 AF XY: 0.000122 AC XY: 8AN XY: 65840
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GnomAD4 exome AF: 0.0000225 AC: 31AN: 1375898Hom.: 1 AF XY: 0.0000353 AC XY: 24AN XY: 678948
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GnomAD4 genome ? AF: 0.00000659 AC: 1AN: 151776Hom.: 0 Cov.: 0 AF XY: 0.0000135 AC XY: 1AN XY: 74188
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at