7-73840121-CTGTG-CTGTGTG
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 4P and 10B. PVS1_StrongBP6_ModerateBS1BS2
The NM_152559.3(METTL27):c.389-3_389-2dupCA variant causes a splice acceptor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0015 in 1,460,744 control chromosomes in the GnomAD database, including 19 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_152559.3 splice_acceptor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
METTL27 | NM_152559.3 | c.389-3_389-2dupCA | splice_acceptor_variant, intron_variant | Intron 4 of 5 | ENST00000297873.9 | NP_689772.2 | ||
METTL27 | XM_017011777.2 | c.389-3_389-2dupCA | splice_acceptor_variant, intron_variant | Intron 4 of 5 | XP_016867266.1 | |||
METTL27 | XM_017011778.2 | c.389-3_389-2dupCA | splice_acceptor_variant, intron_variant | Intron 4 of 5 | XP_016867267.1 | |||
METTL27 | XR_001744563.2 | n.420-3_420-2dupCA | splice_acceptor_variant, intron_variant | Intron 4 of 6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
METTL27 | ENST00000297873.9 | c.389-2_389-1insCA | splice_acceptor_variant, intron_variant | Intron 4 of 5 | 1 | NM_152559.3 | ENSP00000297873.4 | |||
METTL27 | ENST00000458679.5 | n.253-2_253-1insCA | splice_acceptor_variant, intron_variant | Intron 3 of 4 | 4 | ENSP00000398533.1 | ||||
METTL27 | ENST00000493174.1 | n.284-2_284-1insCA | splice_acceptor_variant, intron_variant | Intron 3 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00254 AC: 281AN: 110796Hom.: 4 Cov.: 27
GnomAD3 exomes AF: 0.00166 AC: 351AN: 211532Hom.: 5 AF XY: 0.00160 AC XY: 183AN XY: 114074
GnomAD4 exome AF: 0.00142 AC: 1912AN: 1349888Hom.: 15 Cov.: 34 AF XY: 0.00142 AC XY: 949AN XY: 668946
GnomAD4 genome AF: 0.00253 AC: 280AN: 110856Hom.: 4 Cov.: 27 AF XY: 0.00227 AC XY: 119AN XY: 52468
ClinVar
Submissions by phenotype
not specified Benign:1
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Not reported. No information available. Gene not associated to pt disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at