chr1-36455801-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_031280.4(MRPS15):āc.761A>Cā(p.Lys254Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,730 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_031280.4 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 |
---|---|---|---|---|---|---|---|
MRPS15 | NM_031280.4 | c.761A>C | p.Lys254Thr | missense_variant | 8/8 | ENST00000373116.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRPS15 | ENST00000373116.6 | c.761A>C | p.Lys254Thr | missense_variant | 8/8 | 1 | NM_031280.4 | P1 | |
MRPS15 | ENST00000462067.1 | n.1585A>C | non_coding_transcript_exon_variant | 4/4 | 2 | ||||
MRPS15 | ENST00000477040.1 | n.505A>C | non_coding_transcript_exon_variant | 2/2 | 2 | ||||
MRPS15 | ENST00000488606.5 | n.2098A>C | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461730Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727172
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | The c.761A>C (p.K254T) alteration is located in exon 8 (coding exon 8) of the MRPS15 gene. This alteration results from a A to C substitution at nucleotide position 761, causing the lysine (K) at amino acid position 254 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
Publications
No publications associated with this variant yet.