rs938288
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_031220.4(PITPNM3):c.705C>T(p.Thr235Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 1,613,450 control chromosomes in the GnomAD database, including 281,443 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_031220.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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PITPNM3 | ENST00000262483.13 | c.705C>T | p.Thr235Thr | synonymous_variant | Exon 7 of 20 | 1 | NM_031220.4 | ENSP00000262483.8 | ||
PITPNM3 | ENST00000572795.1 | n.3211C>T | non_coding_transcript_exon_variant | Exon 1 of 14 | 1 | |||||
PITPNM3 | ENST00000421306.7 | c.597C>T | p.Thr199Thr | synonymous_variant | Exon 6 of 19 | 2 | ENSP00000407882.3 |
Frequencies
GnomAD3 genomes AF: 0.505 AC: 76724AN: 151920Hom.: 21194 Cov.: 32
GnomAD3 exomes AF: 0.530 AC: 132573AN: 250108Hom.: 37202 AF XY: 0.536 AC XY: 72508AN XY: 135396
GnomAD4 exome AF: 0.589 AC: 860742AN: 1461412Hom.: 260248 Cov.: 67 AF XY: 0.587 AC XY: 426430AN XY: 726978
GnomAD4 genome AF: 0.505 AC: 76730AN: 152038Hom.: 21195 Cov.: 32 AF XY: 0.503 AC XY: 37357AN XY: 74286
ClinVar
Submissions by phenotype
not provided Benign:3
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not specified Benign:2
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Cone-rod dystrophy 5 Benign:2
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at