chr4-82429443-G-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_031372.4(HNRNPDL):c.248C>A(p.Pro83Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000932 in 1,609,924 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_031372.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HNRNPDL | NM_031372.4 | c.248C>A | p.Pro83Gln | missense_variant | 1/8 | ENST00000295470.10 | NP_112740.1 | |
HNRNPDL | NM_001207000.1 | c.248C>A | p.Pro83Gln | missense_variant | 1/7 | NP_001193929.1 | ||
HNRNPDL | NR_003249.2 | n.783C>A | non_coding_transcript_exon_variant | 1/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HNRNPDL | ENST00000295470.10 | c.248C>A | p.Pro83Gln | missense_variant | 1/8 | 1 | NM_031372.4 | ENSP00000295470 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000396 AC: 6AN: 151694Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000126 AC: 3AN: 237318Hom.: 0 AF XY: 0.00000768 AC XY: 1AN XY: 130142
GnomAD4 exome AF: 0.00000617 AC: 9AN: 1458230Hom.: 0 Cov.: 33 AF XY: 0.00000689 AC XY: 5AN XY: 725278
GnomAD4 genome AF: 0.0000396 AC: 6AN: 151694Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74076
ClinVar
Submissions by phenotype
Autosomal dominant limb-girdle muscular dystrophy type 1G Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jan 31, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at