rs147431889
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The NM_005356.5(LCK):āc.161C>Gā(p.Ser54Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00064 in 1,613,434 control chromosomes in the GnomAD database, including 4 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 (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S54A) has been classified as Uncertain significance.
Frequency
Consequence
NM_005356.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LCK | NM_005356.5 | c.161C>G | p.Ser54Cys | missense_variant | 3/13 | ENST00000336890.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LCK | ENST00000336890.10 | c.161C>G | p.Ser54Cys | missense_variant | 3/13 | 1 | NM_005356.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00352 AC: 535AN: 152112Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000857 AC: 215AN: 250826Hom.: 1 AF XY: 0.000642 AC XY: 87AN XY: 135562
GnomAD4 exome AF: 0.000339 AC: 495AN: 1461204Hom.: 3 Cov.: 32 AF XY: 0.000288 AC XY: 209AN XY: 726844
GnomAD4 genome ? AF: 0.00353 AC: 537AN: 152230Hom.: 1 Cov.: 32 AF XY: 0.00335 AC XY: 249AN XY: 74416
ClinVar
Submissions by phenotype
Severe combined immunodeficiency due to LCK deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 20, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at