chr14-100729022-A-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003836.7(DLK1):c.218A>T(p.Gln73Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00339 in 1,614,052 control chromosomes in the GnomAD database, including 157 homozygotes. In-silico tool predicts 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q73K) has been classified as Uncertain significance.
Frequency
Consequence
NM_003836.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLK1 | NM_003836.7 | c.218A>T | p.Gln73Leu | missense_variant | 3/5 | ENST00000341267.9 | |
DLK1 | NM_001317172.2 | c.218A>T | p.Gln73Leu | missense_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLK1 | ENST00000341267.9 | c.218A>T | p.Gln73Leu | missense_variant | 3/5 | 1 | NM_003836.7 | P1 | |
DLK1 | ENST00000331224.10 | c.218A>T | p.Gln73Leu | missense_variant | 3/6 | 1 | |||
DLK1 | ENST00000556051.1 | c.218A>T | p.Gln73Leu | missense_variant | 3/3 | 2 | |||
DLK1 | ENST00000392848.9 | c.218A>T | p.Gln73Leu | missense_variant | 5/6 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0187 AC: 2837AN: 152116Hom.: 81 Cov.: 32
GnomAD3 exomes AF: 0.00470 AC: 1182AN: 251398Hom.: 28 AF XY: 0.00338 AC XY: 459AN XY: 135882
GnomAD4 exome AF: 0.00180 AC: 2632AN: 1461818Hom.: 76 Cov.: 31 AF XY: 0.00157 AC XY: 1141AN XY: 727212
GnomAD4 genome ? AF: 0.0186 AC: 2838AN: 152234Hom.: 81 Cov.: 32 AF XY: 0.0179 AC XY: 1332AN XY: 74430
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