chr1-107057125-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018137.3(PRMT6):c.410C>T(p.Pro137Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000111 in 1,607,142 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018137.3 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 |
---|---|---|---|---|---|---|---|
PRMT6 | NM_018137.3 | c.410C>T | p.Pro137Leu | missense_variant | 1/1 | ENST00000370078.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRMT6 | ENST00000370078.2 | c.410C>T | p.Pro137Leu | missense_variant | 1/1 | NM_018137.3 | P1 | ||
PRMT6 | ENST00000650338.1 | c.224C>T | p.Pro75Leu | missense_variant, NMD_transcript_variant | 1/3 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000990 AC: 24AN: 242486Hom.: 0 AF XY: 0.0000681 AC XY: 9AN XY: 132178
GnomAD4 exome AF: 0.000120 AC: 174AN: 1454926Hom.: 0 Cov.: 32 AF XY: 0.000123 AC XY: 89AN XY: 724084
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 16, 2023 | The c.410C>T (p.P137L) alteration is located in exon 1 (coding exon 1) of the PRMT6 gene. This alteration results from a C to T substitution at nucleotide position 410, causing the proline (P) at amino acid position 137 to be replaced by a leucine (L). 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