8-10765625-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017884.6(PINX1):c.763G>A(p.Ala255Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000421 in 1,613,724 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PINX1 | NM_017884.6 | c.763G>A | p.Ala255Thr | missense_variant | 7/7 | ENST00000314787.8 | NP_060354.4 | |
LOC102723313 | NR_146188.1 | n.341-2775C>T | intron_variant, non_coding_transcript_variant | |||||
PINX1 | NM_001284356.2 | c.*161G>A | 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.763G>A | p.Ala255Thr | missense_variant | 7/7 | 1 | NM_017884.6 | ENSP00000318966 | P2 | |
ENST00000657150.1 | n.174-2775C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152192Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000482 AC: 12AN: 248812Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135004
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461532Hom.: 0 Cov.: 32 AF XY: 0.0000289 AC XY: 21AN XY: 727068
GnomAD4 genome AF: 0.000184 AC: 28AN: 152192Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 23, 2023 | The c.763G>A (p.A255T) alteration is located in exon 7 (coding exon 7) of the PINX1 gene. This alteration results from a G to A substitution at nucleotide position 763, causing the alanine (A) at amino acid position 255 to be replaced by a threonine (T). 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