chr1-184598402-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_030806.4(C1orf21):āc.268A>Gā(p.Met90Val) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000954 in 1,613,700 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. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_030806.4 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
C1orf21 | NM_030806.4 | c.268A>G | p.Met90Val | missense_variant, splice_region_variant | 5/6 | ENST00000235307.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C1orf21 | ENST00000235307.7 | c.268A>G | p.Met90Val | missense_variant, splice_region_variant | 5/6 | 1 | NM_030806.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000479 AC: 12AN: 250774Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135552
GnomAD4 exome AF: 0.0000924 AC: 135AN: 1461390Hom.: 0 Cov.: 30 AF XY: 0.0000770 AC XY: 56AN XY: 726976
GnomAD4 genome AF: 0.000125 AC: 19AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74480
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 27, 2021 | The c.268A>G (p.M90V) alteration is located in exon 5 (coding exon 4) of the C1orf21 gene. This alteration results from a A to G substitution at nucleotide position 268, causing the methionine (M) at amino acid position 90 to be replaced by a valine (V). 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