17-60150038-C-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_000717.5(CA4):c.4C>A(p.Arg2=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000412 in 1,602,142 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. R2R) has been classified as Likely benign.
Frequency
Consequence
NM_000717.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CA4 | NM_000717.5 | c.4C>A | p.Arg2= | synonymous_variant | 1/8 | ENST00000300900.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CA4 | ENST00000300900.9 | c.4C>A | p.Arg2= | synonymous_variant | 1/8 | 1 | NM_000717.5 | P1 | |
CA4 | ENST00000591725.1 | c.-355C>A | 5_prime_UTR_variant | 1/5 | 3 | ||||
CA4 | ENST00000585705.5 | n.97C>A | non_coding_transcript_exon_variant | 1/3 | 3 | ||||
CA4 | ENST00000586876.1 | c.4C>A | p.Arg2= | synonymous_variant, NMD_transcript_variant | 1/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152260Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000176 AC: 4AN: 226970Hom.: 0 AF XY: 0.00000793 AC XY: 1AN XY: 126052
GnomAD4 exome AF: 0.0000435 AC: 63AN: 1449882Hom.: 0 Cov.: 31 AF XY: 0.0000374 AC XY: 27AN XY: 721698
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152260Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74384
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 23, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at