22-36999842-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001163857.2(CIMIP4):c.632G>A(p.Arg211Gln) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,612,242 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/22 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 Likely benign (★).
Frequency
Consequence
NM_001163857.2 missense, splice_region
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CIMIP4 | NM_001163857.2 | c.632G>A | p.Arg211Gln | missense_variant, splice_region_variant | Exon 4 of 6 | ENST00000381821.2 | NP_001157329.1 | |
CIMIP4 | NM_178552.4 | c.377G>A | p.Arg126Gln | missense_variant, splice_region_variant | Exon 4 of 6 | NP_848647.1 | ||
CIMIP4 | XM_011530165.3 | c.632G>A | p.Arg211Gln | missense_variant, splice_region_variant | Exon 5 of 7 | XP_011528467.1 | ||
CIMIP4 | XM_011530166.2 | c.377G>A | p.Arg126Gln | missense_variant, splice_region_variant | Exon 4 of 6 | XP_011528468.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TEX33 | ENST00000381821.2 | c.632G>A | p.Arg211Gln | missense_variant, splice_region_variant | Exon 4 of 6 | 1 | NM_001163857.2 | ENSP00000371243.1 | ||
TEX33 | ENST00000402860.7 | c.377G>A | p.Arg126Gln | missense_variant, splice_region_variant | Exon 4 of 6 | 1 | ENSP00000385179.3 | |||
TEX33 | ENST00000405091.6 | c.632G>A | p.Arg211Gln | missense_variant, splice_region_variant | Exon 5 of 7 | 5 | ENSP00000386118.2 | |||
TEX33 | ENST00000442538.5 | c.206G>A | p.Arg69Gln | missense_variant, splice_region_variant | Exon 2 of 4 | 3 | ENSP00000406640.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152010Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249512Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134862
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1460232Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726378
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152010Hom.: 0 Cov.: 29 AF XY: 0.0000135 AC XY: 1AN XY: 74236
ClinVar
Submissions by phenotype
not specified Benign:1
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