NM_031372.4:c.356C>T
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_031372.4(HNRNPDL):c.356C>T(p.Thr119Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00215 in 1,613,886 control chromosomes in the GnomAD database, including 59 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 Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T119A) has been classified as Uncertain significance.
Frequency
Consequence
NM_031372.4 missense
Scores
Clinical Significance
Conservation
Publications
- autosomal dominant limb-girdle muscular dystrophy type 1GInheritance: AD Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics
- muscular dystrophy, limb-girdle, autosomal dominantInheritance: AD Classification: MODERATE Submitted by: ClinGen
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ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HNRNPDL | NM_031372.4 | c.356C>T | p.Thr119Ile | missense_variant | Exon 1 of 8 | ENST00000295470.10 | NP_112740.1 | |
HNRNPDL | NM_001207000.1 | c.356C>T | p.Thr119Ile | missense_variant | Exon 1 of 7 | NP_001193929.1 | ||
HNRNPDL | NR_003249.2 | n.891C>T | non_coding_transcript_exon_variant | Exon 1 of 9 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0115 AC: 1744AN: 152166Hom.: 32 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00317 AC: 794AN: 250602 AF XY: 0.00230 show subpopulations
GnomAD4 exome AF: 0.00118 AC: 1724AN: 1461604Hom.: 28 Cov.: 33 AF XY: 0.00100 AC XY: 730AN XY: 727126 show subpopulations
GnomAD4 genome AF: 0.0114 AC: 1740AN: 152282Hom.: 31 Cov.: 32 AF XY: 0.0114 AC XY: 850AN XY: 74458 show subpopulations
ClinVar
Submissions by phenotype
Autosomal dominant limb-girdle muscular dystrophy type 1G Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at