chr5-102867328-G-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001177306.2(PAM):c.145G>C(p.Val49Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0125 in 1,600,974 control chromosomes in the GnomAD database, including 157 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001177306.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAM | NM_001177306.2 | c.145G>C | p.Val49Leu | missense_variant | 3/26 | ENST00000438793.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAM | ENST00000438793.8 | c.145G>C | p.Val49Leu | missense_variant | 3/26 | 1 | NM_001177306.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00928 AC: 1411AN: 152088Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00856 AC: 2150AN: 251190Hom.: 24 AF XY: 0.00856 AC XY: 1162AN XY: 135776
GnomAD4 exome AF: 0.0128 AC: 18566AN: 1448768Hom.: 152 Cov.: 26 AF XY: 0.0126 AC XY: 9063AN XY: 721646
GnomAD4 genome ? AF: 0.00926 AC: 1410AN: 152206Hom.: 5 Cov.: 32 AF XY: 0.00919 AC XY: 684AN XY: 74408
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at