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

Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000075 ( 0 hom. )

Consequence

CRYBG2
NM_001039775.4 missense

Scores

2
13

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.28
Variant links:
Genes affected
CRYBG2 (HGNC:17295): (crystallin beta-gamma domain containing 2) Predicted to enable carbohydrate binding activity. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.060483992).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CRYBG2NM_001039775.4 linkc.4678G>A p.Asp1560Asn missense_variant Exon 18 of 20 ENST00000308182.10 NP_001034864.2 Q8N1P7Q9NWG5
CRYBG2XM_011541673.3 linkc.4849G>A p.Asp1617Asn missense_variant Exon 18 of 20 XP_011539975.1
CRYBG2XM_005245918.3 linkc.4678G>A p.Asp1560Asn missense_variant Exon 18 of 20 XP_005245975.1 Q8N1P7
CRYBG2XM_011541672.2 linkc.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
CRYBG2ENST00000308182.10 linkc.4678G>A p.Asp1560Asn missense_variant Exon 18 of 20 5 NM_001039775.4 ENSP00000310435.6 Q8N1P7
CRYBG2ENST00000475866.3 linkc.5650G>A p.Asp1884Asn missense_variant Exon 20 of 22 4 ENSP00000428746.2 E7ET48
CRYBG2ENST00000374208.1 linkn.156G>A non_coding_transcript_exon_variant Exon 2 of 4 5
CRYBG2ENST00000374211.5 linkn.292G>A non_coding_transcript_exon_variant Exon 2 of 4 3

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD3 exomes
AF:
0.0000200
AC:
5
AN:
250496
Hom.:
0
AF XY:
0.0000221
AC XY:
3
AN XY:
135486
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000289
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.0000653
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000753
AC:
11
AN:
1461070
Hom.:
0
Cov.:
31
AF XY:
0.00000963
AC XY:
7
AN XY:
726880
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000224
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.0000928
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
31
Bravo
AF:
0.00000378
ExAC
AF:
0.00000824
AC:
1

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Oct 08, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.46
T
BayesDel_noAF
Benign
-0.68
CADD
Benign
15
DANN
Uncertain
0.99
Eigen
Benign
-1.0
Eigen_PC
Benign
-1.0
FATHMM_MKL
Benign
0.18
N
LIST_S2
Benign
0.57
T;T
M_CAP
Benign
0.012
T
MetaRNN
Benign
0.060
T;T
MetaSVM
Benign
-1.0
T
PrimateAI
Benign
0.41
T
REVEL
Benign
0.045
Sift4G
Uncertain
0.021
.;D
Vest4
0.19
MVP
0.20
ClinPred
0.060
T
GERP RS
2.6
gMVP
0.26

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs765497988; hg19: chr1-26650702; API