chr16-370060-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006428.5(MRPL28):āc.159C>Gā(p.Asn53Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000366 in 1,612,958 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 (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N53T) has been classified as Uncertain significance.
Frequency
Consequence
NM_006428.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRPL28 | NM_006428.5 | c.159C>G | p.Asn53Lys | missense_variant | 2/6 | ENST00000199706.13 | |
MRPL28 | XM_005255041.3 | c.159C>G | p.Asn53Lys | missense_variant | 2/6 | ||
MRPL28 | XM_011522351.3 | c.159C>G | p.Asn53Lys | missense_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRPL28 | ENST00000199706.13 | c.159C>G | p.Asn53Lys | missense_variant | 2/6 | 1 | NM_006428.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152148Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000322 AC: 8AN: 248274Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134814
GnomAD4 exome AF: 0.0000199 AC: 29AN: 1460692Hom.: 0 Cov.: 34 AF XY: 0.0000179 AC XY: 13AN XY: 726638
GnomAD4 genome AF: 0.000197 AC: 30AN: 152266Hom.: 0 Cov.: 34 AF XY: 0.000202 AC XY: 15AN XY: 74438
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2021 | The c.159C>G (p.N53K) alteration is located in exon 2 (coding exon 1) of the MRPL28 gene. This alteration results from a C to G substitution at nucleotide position 159, causing the asparagine (N) at amino acid position 53 to be replaced by a lysine (K). 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