chr17-47824336-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145255.4(MRPL10):c.655C>T(p.His219Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,461,700 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_145255.4 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 |
---|---|---|---|---|---|---|---|
MRPL10 | NM_145255.4 | c.655C>T | p.His219Tyr | missense_variant | 5/5 | ENST00000351111.7 | |
MRPL10 | NM_148887.3 | c.685C>T | p.His229Tyr | missense_variant | 6/6 | ||
MRPL10 | XM_024450575.2 | c.685C>T | p.His229Tyr | missense_variant | 6/6 | ||
MRPL10 | NR_037575.2 | n.834C>T | non_coding_transcript_exon_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRPL10 | ENST00000351111.7 | c.655C>T | p.His219Tyr | missense_variant | 5/5 | 1 | NM_145255.4 | P1 | |
MRPL10 | ENST00000290208.11 | c.685C>T | p.His229Tyr | missense_variant | 5/5 | 2 | |||
MRPL10 | ENST00000414011.1 | c.685C>T | p.His229Tyr | missense_variant | 6/6 | 3 | |||
MRPL10 | ENST00000421763.5 | c.*657C>T | 3_prime_UTR_variant, NMD_transcript_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251046Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135680
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461700Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 727134
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 19, 2023 | The c.685C>T (p.H229Y) alteration is located in exon 6 (coding exon 5) of the MRPL10 gene. This alteration results from a C to T substitution at nucleotide position 685, causing the histidine (H) at amino acid position 229 to be replaced by a tyrosine (Y). 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