12-7089713-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001733.7(C1R):c.445C>T(p.Arg149Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000525 in 780,708 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_001733.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
C1R | ENST00000647956.2 | c.445C>T | p.Arg149Trp | missense_variant | Exon 4 of 11 | NM_001733.7 | ENSP00000497341.1 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000683 AC: 17AN: 248956Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135054
GnomAD4 exome AF: 0.0000366 AC: 23AN: 628468Hom.: 0 Cov.: 0 AF XY: 0.0000234 AC XY: 8AN XY: 342360
GnomAD4 genome AF: 0.000118 AC: 18AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74386
ClinVar
Submissions by phenotype
not provided Uncertain:1
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Ehlers-Danlos syndrome, periodontal type 1 Uncertain:1
C1R NM_001733.5 exon 4 p.Arg149Trp (c.445C>T): This variant has not been reported in the literature but is present in 0.05% (13/24174) of African alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/12-7242309-G-A?dataset=gnomad_r2_1). Evolutionary conservation suggests that this variant may not impact the protein; computational predictive tools for this variant are unclear. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at