rs4242746
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_014889.4(PITRM1):āc.982A>Gā(p.Ile328Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 1,597,334 control chromosomes in the GnomAD database, including 367,165 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_014889.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PITRM1 | NM_014889.4 | c.982A>G | p.Ile328Val | missense_variant | 9/27 | ENST00000224949.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PITRM1 | ENST00000224949.9 | c.982A>G | p.Ile328Val | missense_variant | 9/27 | 1 | NM_014889.4 | P3 | |
PITRM1-AS1 | ENST00000598280.5 | n.270-4222T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.648 AC: 98393AN: 151918Hom.: 32011 Cov.: 32
GnomAD3 exomes AF: 0.638 AC: 150572AN: 235956Hom.: 48388 AF XY: 0.643 AC XY: 81785AN XY: 127242
GnomAD4 exome AF: 0.679 AC: 981669AN: 1445296Hom.: 335139 Cov.: 30 AF XY: 0.678 AC XY: 487073AN XY: 718210
GnomAD4 genome ? AF: 0.648 AC: 98450AN: 152038Hom.: 32026 Cov.: 32 AF XY: 0.644 AC XY: 47882AN XY: 74304
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at