17-29249184-C-T
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBS1BS2
The NM_005208.5(CRYBA1):c.74C>T(p.Pro25Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0258 in 1,612,402 control chromosomes in the GnomAD database, including 651 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_005208.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CRYBA1 | ENST00000225387.8 | c.74C>T | p.Pro25Leu | missense_variant | Exon 2 of 6 | 1 | NM_005208.5 | ENSP00000225387.3 | ||
CRYBA1 | ENST00000484605.1 | n.62C>T | non_coding_transcript_exon_variant | Exon 2 of 5 | 5 | ENSP00000464368.1 |
Frequencies
GnomAD3 genomes AF: 0.0187 AC: 2838AN: 152082Hom.: 36 Cov.: 31
GnomAD3 exomes AF: 0.0172 AC: 4326AN: 251296Hom.: 43 AF XY: 0.0175 AC XY: 2379AN XY: 135852
GnomAD4 exome AF: 0.0266 AC: 38835AN: 1460202Hom.: 615 Cov.: 29 AF XY: 0.0257 AC XY: 18666AN XY: 726520
GnomAD4 genome AF: 0.0186 AC: 2837AN: 152200Hom.: 36 Cov.: 31 AF XY: 0.0176 AC XY: 1311AN XY: 74402
ClinVar
Submissions by phenotype
not provided Benign:2
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See Variant Classification Assertion Criteria. -
not specified Benign:1
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Cataract 10 multiple types Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at