5-102925031-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001177306.2(PAM):c.431G>A(p.Arg144Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000853 in 1,560,062 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001177306.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PAM | NM_001177306.2 | c.431G>A | p.Arg144Gln | missense_variant | 6/26 | ENST00000438793.8 | NP_001170777.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PAM | ENST00000438793.8 | c.431G>A | p.Arg144Gln | missense_variant | 6/26 | 1 | NM_001177306.2 | ENSP00000396493.3 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152062Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000231 AC: 58AN: 251172Hom.: 3 AF XY: 0.000199 AC XY: 27AN XY: 135868
GnomAD4 exome AF: 0.0000753 AC: 106AN: 1407880Hom.: 1 Cov.: 24 AF XY: 0.0000739 AC XY: 52AN XY: 703750
GnomAD4 genome AF: 0.000177 AC: 27AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74396
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 15, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at