chr1-17338121-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_012387.3(PADI4):c.492G>A(p.Met164Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000184 in 1,612,584 control chromosomes in the GnomAD database, including 2 homozygotes. 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M164T) has been classified as Benign.
Frequency
Consequence
NM_012387.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PADI4 | NM_012387.3 | c.492G>A | p.Met164Ile | missense_variant | 5/16 | ENST00000375448.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PADI4 | ENST00000375448.4 | c.492G>A | p.Met164Ile | missense_variant | 5/16 | 1 | NM_012387.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000386 AC: 97AN: 251466Hom.: 1 AF XY: 0.000368 AC XY: 50AN XY: 135904
GnomAD4 exome AF: 0.000190 AC: 278AN: 1460410Hom.: 2 Cov.: 29 AF XY: 0.000226 AC XY: 164AN XY: 726550
GnomAD4 genome AF: 0.000118 AC: 18AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 11, 2022 | The c.492G>A (p.M164I) alteration is located in exon 5 (coding exon 5) of the PADI4 gene. This alteration results from a G to A substitution at nucleotide position 492, causing the methionine (M) at amino acid position 164 to be replaced by an isoleucine (I). 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