rs369755712
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001018116.2(CAVIN4):c.-10A>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,528 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_001018116.2 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAVIN4 | NM_001018116.2 | c.-10A>T | 5_prime_UTR_variant | Exon 1 of 2 | ENST00000307584.6 | NP_001018126.1 | ||
CAVIN4 | XM_047423346.1 | c.22-55A>T | intron_variant | Intron 1 of 2 | XP_047279302.1 | |||
CAVIN4 | XM_047423347.1 | c.21+1179A>T | intron_variant | Intron 1 of 1 | XP_047279303.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250762Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135538
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461200Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 726928
GnomAD4 genome AF: 0.000105 AC: 16AN: 152328Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74494
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.-10A>T variant in MURC has not been previously reported in individuals wit h cardiomyopathy, but has been identified in 0.1% (9/10366) of African chromosom es by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; db SNP rs369755712). Although this variant is outside of the coding sequence, it re sides in the promoter region upstream of the translation start site and an impac t to transcription cannot be ruled out. In summary, the clinical significance of the c.-10A>T variant is uncertain. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at