1-26324211-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.4678G>A(p.Asp1560Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000753 in 1,461,070 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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.4678G>A | p.Asp1560Asn | missense_variant | Exon 18 of 20 | ENST00000308182.10 | NP_001034864.2 | |
CRYBG2 | XM_011541673.3 | c.4849G>A | p.Asp1617Asn | missense_variant | Exon 18 of 20 | XP_011539975.1 | ||
CRYBG2 | XM_005245918.3 | c.4678G>A | p.Asp1560Asn | missense_variant | Exon 18 of 20 | XP_005245975.1 | ||
CRYBG2 | XM_011541672.2 | c.4642G>A | p.Asp1548Asn | missense_variant | Exon 17 of 19 | XP_011539974.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CRYBG2 | ENST00000308182.10 | c.4678G>A | p.Asp1560Asn | missense_variant | Exon 18 of 20 | 5 | NM_001039775.4 | ENSP00000310435.6 | ||
CRYBG2 | ENST00000475866.3 | c.5650G>A | p.Asp1884Asn | missense_variant | Exon 20 of 22 | 4 | ENSP00000428746.2 | |||
CRYBG2 | ENST00000374208.1 | n.156G>A | non_coding_transcript_exon_variant | Exon 2 of 4 | 5 | |||||
CRYBG2 | ENST00000374211.5 | n.292G>A | non_coding_transcript_exon_variant | Exon 2 of 4 | 3 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 250496Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135486
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461070Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 726880
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4678G>A (p.D1560N) alteration is located in exon 18 (coding exon 17) of the AIM1L gene. This alteration results from a G to A substitution at nucleotide position 4678, causing the aspartic acid (D) at amino acid position 1560 to be replaced by an asparagine (N). 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