rs17711777
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_017884.6(PINX1):āc.658A>Gā(p.Thr220Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.066 in 1,613,944 control chromosomes in the GnomAD database, including 4,478 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_017884.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PINX1 | NM_017884.6 | c.658A>G | p.Thr220Ala | missense_variant | 7/7 | ENST00000314787.8 | NP_060354.4 | |
PINX1 | NM_001284356.2 | c.*56A>G | 3_prime_UTR_variant | 6/6 | NP_001271285.1 | |||
LOC102723313 | NR_146188.1 | n.341-2670T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PINX1 | ENST00000314787.8 | c.658A>G | p.Thr220Ala | missense_variant | 7/7 | 1 | NM_017884.6 | ENSP00000318966.3 | ||
PINX1 | ENST00000554914.1 | c.395-39064A>G | intron_variant | 2 | ENSP00000451145.1 |
Frequencies
GnomAD3 genomes AF: 0.0530 AC: 8066AN: 152170Hom.: 339 Cov.: 33
GnomAD3 exomes AF: 0.0725 AC: 18064AN: 249206Hom.: 1202 AF XY: 0.0663 AC XY: 8959AN XY: 135212
GnomAD4 exome AF: 0.0674 AC: 98448AN: 1461656Hom.: 4132 Cov.: 34 AF XY: 0.0656 AC XY: 47686AN XY: 727114
GnomAD4 genome AF: 0.0531 AC: 8081AN: 152288Hom.: 346 Cov.: 33 AF XY: 0.0534 AC XY: 3977AN XY: 74464
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at