chr8-10765720-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017884.6(PINX1):c.668A>T(p.Asp223Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,638 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PINX1 | NM_017884.6 | c.668A>T | p.Asp223Val | missense_variant | 7/7 | ENST00000314787.8 | |
LOC102723313 | NR_146188.1 | n.341-2680T>A | intron_variant, non_coding_transcript_variant | ||||
PINX1 | NM_001284356.2 | c.*66A>T | 3_prime_UTR_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PINX1 | ENST00000314787.8 | c.668A>T | p.Asp223Val | missense_variant | 7/7 | 1 | NM_017884.6 | P2 | |
ENST00000657150.1 | n.174-2680T>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461638Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727094
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2023 | The c.668A>T (p.D223V) alteration is located in exon 7 (coding exon 7) of the PINX1 gene. This alteration results from a A to T substitution at nucleotide position 668, causing the aspartic acid (D) at amino acid position 223 to be replaced by a valine (V). 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