13-102686054-T-TA
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_001010977.3(METTL21C):c.771_772insT(p.Lys258Ter) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000249 in 1,589,610 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00014 ( 1 hom. )
Consequence
METTL21C
NM_001010977.3 frameshift
NM_001010977.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0650
Genes affected
METTL21C (HGNC:33717): (methyltransferase 21C, AARS1 lysine) Enables heat shock protein binding activity and protein-lysine N-methyltransferase activity. Involved in protein methylation. Located in nucleus. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 13-102686054-T-TA is Benign according to our data. Variant chr13-102686054-T-TA is described in ClinVar as [Likely_benign]. Clinvar id is 779647.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
METTL21C | NM_001010977.3 | c.771_772insT | p.Lys258Ter | frameshift_variant | 4/4 | ENST00000267273.7 | |
METTL21C | XM_047430117.1 | c.771_772insT | p.Lys258Ter | frameshift_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
METTL21C | ENST00000267273.7 | c.771_772insT | p.Lys258Ter | frameshift_variant | 4/4 | 1 | NM_001010977.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00131 AC: 200AN: 152204Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
200
AN:
152204
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000350 AC: 83AN: 237348Hom.: 0 AF XY: 0.000250 AC XY: 32AN XY: 127886
GnomAD3 exomes
AF:
AC:
83
AN:
237348
Hom.:
AF XY:
AC XY:
32
AN XY:
127886
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000137 AC: 197AN: 1437288Hom.: 1 Cov.: 31 AF XY: 0.000126 AC XY: 90AN XY: 711472
GnomAD4 exome
AF:
AC:
197
AN:
1437288
Hom.:
Cov.:
31
AF XY:
AC XY:
90
AN XY:
711472
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00131 AC: 199AN: 152322Hom.: 0 Cov.: 32 AF XY: 0.00126 AC XY: 94AN XY: 74486
GnomAD4 genome
AF:
AC:
199
AN:
152322
Hom.:
Cov.:
32
AF XY:
AC XY:
94
AN XY:
74486
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1
AN:
3476
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 26, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at