6-16145094-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_013262.4(MYLIP):āc.1025A>Gā(p.Asn342Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 1,613,978 control chromosomes in the GnomAD database, including 237,883 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_013262.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYLIP | NM_013262.4 | c.1025A>G | p.Asn342Ser | missense_variant | 6/7 | ENST00000356840.8 | NP_037394.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYLIP | ENST00000356840.8 | c.1025A>G | p.Asn342Ser | missense_variant | 6/7 | 1 | NM_013262.4 | ENSP00000349298.3 | ||
MYLIP | ENST00000349606.4 | c.482A>G | p.Asn161Ser | missense_variant | 5/6 | 1 | ENSP00000008686.6 |
Frequencies
GnomAD3 genomes AF: 0.633 AC: 96171AN: 152006Hom.: 33227 Cov.: 33
GnomAD3 exomes AF: 0.600 AC: 150922AN: 251402Hom.: 48765 AF XY: 0.587 AC XY: 79722AN XY: 135872
GnomAD4 exome AF: 0.515 AC: 752166AN: 1461854Hom.: 204589 Cov.: 72 AF XY: 0.516 AC XY: 375521AN XY: 727224
GnomAD4 genome AF: 0.633 AC: 96301AN: 152124Hom.: 33294 Cov.: 33 AF XY: 0.633 AC XY: 47055AN XY: 74364
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at