chr21-25593941-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017446.4(MRPL39):c.719T>C(p.Ile240Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000465 in 1,613,520 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017446.4 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 |
---|---|---|---|---|---|---|---|
MRPL39 | NM_017446.4 | c.719T>C | p.Ile240Thr | missense_variant | 7/10 | ENST00000352957.9 | |
MRPL39 | NM_080794.4 | c.719T>C | p.Ile240Thr | missense_variant | 7/11 | ||
MRPL39 | XM_006724026.5 | c.719T>C | p.Ile240Thr | missense_variant | 7/10 | ||
MRPL39 | XM_011529651.3 | c.593T>C | p.Ile198Thr | missense_variant | 7/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRPL39 | ENST00000352957.9 | c.719T>C | p.Ile240Thr | missense_variant | 7/10 | 1 | NM_017446.4 | P1 | |
MRPL39 | ENST00000307301.11 | c.719T>C | p.Ile240Thr | missense_variant | 7/11 | 5 | |||
MRPL39 | ENST00000419219.1 | c.689T>C | p.Ile230Thr | missense_variant | 7/8 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251022Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135710
GnomAD4 exome AF: 0.0000486 AC: 71AN: 1461310Hom.: 0 Cov.: 30 AF XY: 0.0000481 AC XY: 35AN XY: 726992
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152210Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 25, 2023 | The c.719T>C (p.I240T) alteration is located in exon 7 (coding exon 7) of the MRPL39 gene. This alteration results from a T to C substitution at nucleotide position 719, causing the isoleucine (I) at amino acid position 240 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