10-3149631-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_014889.4(PITRM1):c.1861G>A(p.Val621Ile) variant causes a missense change. The variant allele was found at a frequency of 0.165 in 1,566,790 control chromosomes in the GnomAD database, including 22,192 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Synonymous variant affecting the same amino acid position (i.e. V621V) has been classified as Likely benign.
Frequency
Consequence
NM_014889.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PITRM1 | NM_014889.4 | c.1861G>A | p.Val621Ile | missense_variant | 16/27 | ENST00000224949.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PITRM1 | ENST00000224949.9 | c.1861G>A | p.Val621Ile | missense_variant | 16/27 | 1 | NM_014889.4 | P3 | |
PITRM1-AS1 | ENST00000598280.5 | n.269+5645C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.150 AC: 22716AN: 151922Hom.: 1762 Cov.: 32
GnomAD3 exomes AF: 0.144 AC: 30838AN: 213836Hom.: 2496 AF XY: 0.148 AC XY: 17196AN XY: 116250
GnomAD4 exome AF: 0.167 AC: 235926AN: 1414750Hom.: 20429 Cov.: 31 AF XY: 0.167 AC XY: 116664AN XY: 700340
GnomAD4 genome AF: 0.149 AC: 22714AN: 152040Hom.: 1763 Cov.: 32 AF XY: 0.149 AC XY: 11055AN XY: 74310
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 28, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
PITRM1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 19, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at