chr1-156908735-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001080471.3(PEAR1):c.1196C>T(p.Thr399Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000709 in 1,410,974 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001080471.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PEAR1 | NM_001080471.3 | c.1196C>T | p.Thr399Met | missense_variant | 10/23 | ENST00000292357.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEAR1 | ENST00000292357.8 | c.1196C>T | p.Thr399Met | missense_variant | 10/23 | 5 | NM_001080471.3 | P1 | |
PEAR1 | ENST00000338302.7 | c.1196C>T | p.Thr399Met | missense_variant | 11/24 | 5 | P1 | ||
PEAR1 | ENST00000469390.5 | n.924C>T | non_coding_transcript_exon_variant | 5/18 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 7.09e-7 AC: 1AN: 1410974Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 698656
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2024 | The c.1196C>T (p.T399M) alteration is located in exon 10 (coding exon 9) of the PEAR1 gene. This alteration results from a C to T substitution at nucleotide position 1196, causing the threonine (T) at amino acid position 399 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at