chr6-2688921-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001012418.5(MYLK4):c.271C>A(p.Arg91Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000235 in 1,614,192 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R91H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001012418.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYLK4 | NM_001012418.5 | c.271C>A | p.Arg91Ser | missense_variant | 4/13 | ENST00000274643.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYLK4 | ENST00000274643.9 | c.271C>A | p.Arg91Ser | missense_variant | 4/13 | 1 | NM_001012418.5 | A2 | |
MYLK4 | ENST00000698899.1 | c.439C>A | p.Arg147Ser | missense_variant | 4/13 | A2 | |||
MYLK4 | ENST00000647417.1 | c.253C>A | p.Arg85Ser | missense_variant | 3/12 | P2 | |||
MYLK4 | ENST00000698900.1 | n.532C>A | non_coding_transcript_exon_variant | 5/9 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251476Hom.: 0 AF XY: 0.0000441 AC XY: 6AN XY: 135908
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461856Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 727226
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152336Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74498
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 07, 2023 | The c.271C>A (p.R91S) alteration is located in exon 4 (coding exon 3) of the MYLK4 gene. This alteration results from a C to A substitution at nucleotide position 271, causing the arginine (R) at amino acid position 91 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at