11-2300760-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000456145.2(C11orf21):c.115C>T(p.Leu39Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000845 in 1,550,666 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000456145.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C11orf21 | NM_001329958.2 | c.54-147C>T | intron_variant | ENST00000381153.8 | |||
C11orf21 | NM_001142946.3 | c.115C>T | p.Leu39Phe | missense_variant | 2/5 | ||
C11orf21 | NR_138249.2 | n.260-1053C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C11orf21 | ENST00000456145.2 | c.115C>T | p.Leu39Phe | missense_variant | 2/5 | 1 | P2 | ||
C11orf21 | ENST00000381153.8 | c.54-147C>T | intron_variant | 1 | NM_001329958.2 | A2 | |||
C11orf21 | ENST00000470369.1 | n.1113C>T | non_coding_transcript_exon_variant | 1/2 | 5 | ||||
C11orf21 | ENST00000495467.1 | n.169-1053C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000260 AC: 4AN: 153968Hom.: 0 AF XY: 0.0000367 AC XY: 3AN XY: 81722
GnomAD4 exome AF: 0.0000880 AC: 123AN: 1398512Hom.: 0 Cov.: 32 AF XY: 0.0000855 AC XY: 59AN XY: 689770
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74310
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 29, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at