17-29246901-A-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_005208.5(CRYBA1):c.31+7A>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000621 in 1,610,258 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_005208.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CRYBA1 | ENST00000225387.8 | c.31+7A>C | splice_region_variant, intron_variant | Intron 1 of 5 | 1 | NM_005208.5 | ENSP00000225387.3 | |||
CRYBA1 | ENST00000484605.1 | n.19+7A>C | splice_region_variant, intron_variant | Intron 1 of 4 | 5 | ENSP00000464368.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000124 AC: 3AN: 242472Hom.: 0 AF XY: 0.0000229 AC XY: 3AN XY: 131088
GnomAD4 exome AF: 0.0000672 AC: 98AN: 1458068Hom.: 0 Cov.: 31 AF XY: 0.0000772 AC XY: 56AN XY: 725012
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74358
ClinVar
Submissions by phenotype
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at