8-10765540-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017884.6(PINX1):c.848C>T(p.Pro283Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,613,480 control chromosomes in the GnomAD database, including 1 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 Uncertain significance (★).
Frequency
Consequence
NM_017884.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PINX1 | NM_017884.6 | c.848C>T | p.Pro283Leu | missense_variant | 7/7 | ENST00000314787.8 | NP_060354.4 | |
LOC102723313 | NR_146188.1 | n.341-2860G>A | intron_variant, non_coding_transcript_variant | |||||
PINX1 | NM_001284356.2 | c.*246C>T | 3_prime_UTR_variant | 6/6 | NP_001271285.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PINX1 | ENST00000314787.8 | c.848C>T | p.Pro283Leu | missense_variant | 7/7 | 1 | NM_017884.6 | ENSP00000318966 | P2 | |
ENST00000657150.1 | n.174-2860G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152070Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000321 AC: 8AN: 248896Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135062
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461410Hom.: 1 Cov.: 32 AF XY: 0.0000248 AC XY: 18AN XY: 727006
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152070Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74256
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2023 | The c.848C>T (p.P283L) alteration is located in exon 7 (coding exon 7) of the PINX1 gene. This alteration results from a C to T substitution at nucleotide position 848, causing the proline (P) at amino acid position 283 to be replaced by a leucine (L). 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