rs7250947
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001367868.2(PLIN4):c.3442C>T(p.Arg1148Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0821 in 1,480,548 control chromosomes in the GnomAD database, including 5,534 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1148H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001367868.2 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 | UniProt |
---|---|---|---|---|---|---|---|
PLIN4 | NM_001367868.2 | c.3442C>T | p.Arg1148Cys | missense_variant | 5/8 | ENST00000301286.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLIN4 | ENST00000301286.5 | c.3442C>T | p.Arg1148Cys | missense_variant | 5/8 | 5 | NM_001367868.2 | P1 | |
PLIN4 | ENST00000633942.1 | c.3445C>T | p.Arg1149Cys | missense_variant | 5/8 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0907 AC: 13798AN: 152160Hom.: 710 Cov.: 33
GnomAD3 exomes AF: 0.0685 AC: 11074AN: 161756Hom.: 485 AF XY: 0.0672 AC XY: 5794AN XY: 86262
GnomAD4 exome AF: 0.0811 AC: 107726AN: 1328270Hom.: 4823 Cov.: 36 AF XY: 0.0795 AC XY: 51443AN XY: 647408
GnomAD4 genome ? AF: 0.0907 AC: 13806AN: 152278Hom.: 711 Cov.: 33 AF XY: 0.0863 AC XY: 6428AN XY: 74456
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at