6-16143722-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_013262.4(MYLIP):c.686T>C(p.Met229Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000651 in 1,614,000 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. M229V) has been classified as Uncertain significance.
Frequency
Consequence
NM_013262.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYLIP | NM_013262.4 | c.686T>C | p.Met229Thr | missense_variant | 5/7 | ENST00000356840.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYLIP | ENST00000356840.8 | c.686T>C | p.Met229Thr | missense_variant | 5/7 | 1 | NM_013262.4 | P1 | |
MYLIP | ENST00000349606.4 | c.143T>C | p.Met48Thr | missense_variant | 4/6 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000111 AC: 28AN: 251450Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135894
GnomAD4 exome AF: 0.0000650 AC: 95AN: 1461866Hom.: 0 Cov.: 31 AF XY: 0.0000756 AC XY: 55AN XY: 727232
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 06, 2021 | The c.686T>C (p.M229T) alteration is located in exon 5 (coding exon 5) of the MYLIP gene. This alteration results from a T to C substitution at nucleotide position 686, causing the methionine (M) at amino acid position 229 to be replaced by a threonine (T). 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