rs34162630
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001256789.3(CACNA1F):c.1523G>A(p.Arg508Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0233 in 1,188,489 control chromosomes in the GnomAD database, including 258 homozygotes. There are 9,016 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001256789.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1F | NM_001256789.3 | c.1523G>A | p.Arg508Gln | missense_variant | Exon 13 of 48 | ENST00000323022.10 | NP_001243718.1 | |
CACNA1F | NM_005183.4 | c.1556G>A | p.Arg519Gln | missense_variant | Exon 13 of 48 | NP_005174.2 | ||
CACNA1F | NM_001256790.3 | c.1361G>A | p.Arg454Gln | missense_variant | Exon 13 of 48 | NP_001243719.1 | ||
CACNA1F | XM_011543983.3 | c.1361G>A | p.Arg454Gln | missense_variant | Exon 13 of 47 | XP_011542285.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1F | ENST00000323022.10 | c.1523G>A | p.Arg508Gln | missense_variant | Exon 13 of 48 | 1 | NM_001256789.3 | ENSP00000321618.6 | ||
CACNA1F | ENST00000376265.2 | c.1556G>A | p.Arg519Gln | missense_variant | Exon 13 of 48 | 1 | ENSP00000365441.2 | |||
CACNA1F | ENST00000376251.5 | c.1361G>A | p.Arg454Gln | missense_variant | Exon 13 of 48 | 1 | ENSP00000365427.1 |
Frequencies
GnomAD3 genomes AF: 0.0175 AC: 1939AN: 110895Hom.: 28 Cov.: 23 AF XY: 0.0174 AC XY: 577AN XY: 33207
GnomAD3 exomes AF: 0.0174 AC: 2498AN: 143850Hom.: 28 AF XY: 0.0183 AC XY: 809AN XY: 44266
GnomAD4 exome AF: 0.0239 AC: 25796AN: 1077547Hom.: 230 Cov.: 32 AF XY: 0.0240 AC XY: 8440AN XY: 351193
GnomAD4 genome AF: 0.0174 AC: 1935AN: 110942Hom.: 28 Cov.: 23 AF XY: 0.0173 AC XY: 576AN XY: 33266
ClinVar
Submissions by phenotype
not provided Benign:3
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not specified Benign:2
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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: Frequency in ESP (all): 180/10956=1.64% -
Congenital stationary night blindness 2A Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at