1-26322050-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001039775.4(CRYBG2):c.4904G>A(p.Arg1635Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000199 in 1,606,248 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1635W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001039775.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CRYBG2 | NM_001039775.4 | c.4904G>A | p.Arg1635Gln | missense_variant | Exon 20 of 20 | ENST00000308182.10 | NP_001034864.2 | |
CRYBG2 | XM_011541673.3 | c.5075G>A | p.Arg1692Gln | missense_variant | Exon 20 of 20 | XP_011539975.1 | ||
CRYBG2 | XM_005245918.3 | c.4904G>A | p.Arg1635Gln | missense_variant | Exon 20 of 20 | XP_005245975.1 | ||
CRYBG2 | XM_011541672.2 | c.4868G>A | p.Arg1623Gln | missense_variant | Exon 19 of 19 | XP_011539974.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CRYBG2 | ENST00000308182.10 | c.4904G>A | p.Arg1635Gln | missense_variant | Exon 20 of 20 | 5 | NM_001039775.4 | ENSP00000310435.6 | ||
CRYBG2 | ENST00000475866.3 | c.5876G>A | p.Arg1959Gln | missense_variant | Exon 22 of 22 | 4 | ENSP00000428746.2 | |||
CRYBG2 | ENST00000374208.1 | n.382G>A | non_coding_transcript_exon_variant | Exon 4 of 4 | 5 | |||||
CRYBG2 | ENST00000374211.5 | n.518G>A | non_coding_transcript_exon_variant | Exon 4 of 4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000360 AC: 9AN: 249802Hom.: 0 AF XY: 0.0000445 AC XY: 6AN XY: 134936
GnomAD4 exome AF: 0.0000199 AC: 29AN: 1454016Hom.: 0 Cov.: 29 AF XY: 0.0000319 AC XY: 23AN XY: 721516
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74438
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4904G>A (p.R1635Q) alteration is located in exon 20 (coding exon 19) of the AIM1L gene. This alteration results from a G to A substitution at nucleotide position 4904, causing the arginine (R) at amino acid position 1635 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at