chr12-7091446-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001733.7(C1R):c.231+6G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0011 in 754,606 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001733.7 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
C1R | ENST00000647956.2 | c.231+6G>A | splice_region_variant, intron_variant | Intron 2 of 10 | NM_001733.7 | ENSP00000497341.1 |
Frequencies
GnomAD3 genomes AF: 0.00312 AC: 475AN: 152178Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.000896 AC: 188AN: 209912Hom.: 1 AF XY: 0.000736 AC XY: 83AN XY: 112722
GnomAD4 exome AF: 0.000584 AC: 352AN: 602310Hom.: 1 Cov.: 0 AF XY: 0.000490 AC XY: 160AN XY: 326638
GnomAD4 genome AF: 0.00313 AC: 477AN: 152296Hom.: 3 Cov.: 32 AF XY: 0.00312 AC XY: 232AN XY: 74474
ClinVar
Submissions by phenotype
Ehlers-Danlos syndrome, periodontal type 1 Benign:1
This variant has not been reported in the literature but is present in the Genome Aggregation Database (Highest reported MAF 1.0% (416/41446) including 2 homozygotes (https://gnomad.broadinstitute.org/variant/12-7091446-C-T?dataset=gnomad_r3). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. This variant is an intronic variant with no predicted change in the amino acid sequence but may have an unknown effect on splicing. Splice prediction tools do not suggest that this variant may affect splicing. However, further studies are needed to understand its impact. In summary, data on this variant suggests that this variant does not cause disease but requires further evidence. Therefore, this variant is classified as likely benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at