14-105529712-TGCCGCCGCCGCC-TGCCGCCGCC
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_025268.4(TMEM121):c.896_898delCGC(p.Pro299del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 1,524,964 control chromosomes in the GnomAD database, including 66,989 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.38 ( 13184 hom., cov: 0)
Exomes 𝑓: 0.27 ( 53805 hom. )
Consequence
TMEM121
NM_025268.4 disruptive_inframe_deletion
NM_025268.4 disruptive_inframe_deletion
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Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.501
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.377 AC: 57185AN: 151606Hom.: 13129 Cov.: 0
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GnomAD3 exomes AF: 0.299 AC: 35606AN: 118980Hom.: 6254 AF XY: 0.299 AC XY: 19684AN XY: 65840
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GnomAD4 exome AF: 0.271 AC: 371787AN: 1373250Hom.: 53805 AF XY: 0.270 AC XY: 182936AN XY: 677610
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GnomAD4 genome AF: 0.378 AC: 57287AN: 151714Hom.: 13184 Cov.: 0 AF XY: 0.374 AC XY: 27719AN XY: 74158
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ClinVar
Not reported inComputational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at