chrX-49205211-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001256789.3(CACNA1F):c.5827G>A(p.Asp1943Asn) variant causes a missense change. The variant allele was found at a frequency of 0.000125 in 1,209,136 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 51 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D1943H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001256789.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1F | NM_001256789.3 | c.5827G>A | p.Asp1943Asn | missense_variant | 48/48 | ENST00000323022.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1F | ENST00000323022.10 | c.5827G>A | p.Asp1943Asn | missense_variant | 48/48 | 1 | NM_001256789.3 | ||
CACNA1F | ENST00000376265.2 | c.5860G>A | p.Asp1954Asn | missense_variant | 48/48 | 1 | P1 | ||
CACNA1F | ENST00000376251.5 | c.5665G>A | p.Asp1889Asn | missense_variant | 48/48 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000805 AC: 9AN: 111750Hom.: 0 Cov.: 23 AF XY: 0.000148 AC XY: 5AN XY: 33898
GnomAD3 exomes AF: 0.000319 AC: 58AN: 182064Hom.: 0 AF XY: 0.000195 AC XY: 13AN XY: 66774
GnomAD4 exome AF: 0.000129 AC: 142AN: 1097386Hom.: 0 Cov.: 30 AF XY: 0.000127 AC XY: 46AN XY: 362788
GnomAD4 genome ? AF: 0.0000805 AC: 9AN: 111750Hom.: 0 Cov.: 23 AF XY: 0.000148 AC XY: 5AN XY: 33898
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 22, 2023 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Oct 01, 2014 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at