rs141010716
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001256789.3(CACNA1F):c.1870G>A(p.Val624Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00316 in 1,160,649 control chromosomes in the GnomAD database, including 8 homozygotes. There are 1,109 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).
Frequency
Consequence
NM_001256789.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1F | NM_001256789.3 | c.1870G>A | p.Val624Ile | missense_variant | Exon 14 of 48 | ENST00000323022.10 | NP_001243718.1 | |
CACNA1F | NM_005183.4 | c.1903G>A | p.Val635Ile | missense_variant | Exon 14 of 48 | NP_005174.2 | ||
CACNA1F | NM_001256790.3 | c.1708G>A | p.Val570Ile | missense_variant | Exon 14 of 48 | NP_001243719.1 | ||
CACNA1F | XM_011543983.3 | c.1708G>A | p.Val570Ile | missense_variant | Exon 14 of 47 | XP_011542285.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1F | ENST00000323022.10 | c.1870G>A | p.Val624Ile | missense_variant | Exon 14 of 48 | 1 | NM_001256789.3 | ENSP00000321618.6 | ||
CACNA1F | ENST00000376265.2 | c.1903G>A | p.Val635Ile | missense_variant | Exon 14 of 48 | 1 | ENSP00000365441.2 | |||
CACNA1F | ENST00000376251.5 | c.1708G>A | p.Val570Ile | missense_variant | Exon 14 of 48 | 1 | ENSP00000365427.1 |
Frequencies
GnomAD3 genomes AF: 0.00227 AC: 252AN: 110862Hom.: 0 Cov.: 21 AF XY: 0.00190 AC XY: 63AN XY: 33088
GnomAD3 exomes AF: 0.00206 AC: 265AN: 128537Hom.: 0 AF XY: 0.00199 AC XY: 83AN XY: 41733
GnomAD4 exome AF: 0.00326 AC: 3421AN: 1049733Hom.: 8 Cov.: 28 AF XY: 0.00313 AC XY: 1046AN XY: 334273
GnomAD4 genome AF: 0.00227 AC: 252AN: 110916Hom.: 0 Cov.: 21 AF XY: 0.00190 AC XY: 63AN XY: 33152
ClinVar
Submissions by phenotype
not specified Benign:4
- -
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Variant has been reported in unknown number of patients with XL congenital stationary night blindness (Weleber 2002 - from abstract, full text not available). MAF 0.6%, 6 hem in ExAC. Status PASS, but relatively poorly covered (51/9104 Eur chr). -
- -
- -
not provided Uncertain:1Benign:2
- -
- -
- -
Congenital stationary night blindness 2A Benign:1
- -
Retinal dystrophy Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at