chr3-97876178-C-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_153605.4(CRYBG3):c.4984C>A(p.Pro1662Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00311 in 1,231,808 control chromosomes in the GnomAD database, including 80 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_153605.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRYBG3 | NM_153605.4 | c.4984C>A | p.Pro1662Thr | missense_variant | 4/22 | ENST00000389622.7 | |
CRYBG3 | XM_005247117.5 | c.4111C>A | p.Pro1371Thr | missense_variant | 3/21 | ||
CRYBG3 | XM_047447439.1 | c.4984C>A | p.Pro1662Thr | missense_variant | 4/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRYBG3 | ENST00000389622.7 | c.4984C>A | p.Pro1662Thr | missense_variant | 4/22 | 5 | NM_153605.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0150 AC: 2278AN: 151902Hom.: 50 Cov.: 32
GnomAD4 exome AF: 0.00143 AC: 1542AN: 1079786Hom.: 30 Cov.: 35 AF XY: 0.00130 AC XY: 662AN XY: 509754
GnomAD4 genome ? AF: 0.0150 AC: 2287AN: 152022Hom.: 50 Cov.: 32 AF XY: 0.0144 AC XY: 1073AN XY: 74308
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 23, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at