6-36961962-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153370.3(PI16):āc.580A>Gā(p.Asn194Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,613,850 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_153370.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PI16 | ENST00000373674.4 | c.580A>G | p.Asn194Asp | missense_variant | 4/7 | 1 | NM_153370.3 | ENSP00000362778.3 | ||
PI16 | ENST00000611814.4 | c.580A>G | p.Asn194Asp | missense_variant | 5/8 | 5 | ENSP00000478888.1 | |||
PI16 | ENST00000647861.1 | c.580A>G | p.Asn194Asp | missense_variant | 6/9 | ENSP00000497550.1 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251384Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135904
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461700Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727180
GnomAD4 genome AF: 0.000118 AC: 18AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 17, 2023 | The c.580A>G (p.N194D) alteration is located in exon 4 (coding exon 4) of the PI16 gene. This alteration results from a A to G substitution at nucleotide position 580, causing the asparagine (N) at amino acid position 194 to be replaced by an aspartic acid (D). 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