chr6-106571412-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001371242.2(CRYBG1):​c.*2846C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,378 control chromosomes in the GnomAD database, including 2,477 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.16 ( 2476 hom., cov: 32)
Exomes 𝑓: 0.11 ( 1 hom. )

Consequence

CRYBG1
NM_001371242.2 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.597
Variant links:
Genes affected
CRYBG1 (HGNC:356): (crystallin beta-gamma domain containing 1) Predicted to enable carbohydrate binding activity. [provided by Alliance of Genome Resources, Apr 2022]
RTN4IP1 (HGNC:18647): (reticulon 4 interacting protein 1) This gene encodes a mitochondrial protein that interacts with reticulon 4, which is a potent inhibitor of regeneration following spinal cord injury. This interaction may be important for reticulon-induced inhibition of neurite growth. Mutations in this gene can cause optic atrophy 10, with or without ataxia, cognitive disability, and seizures. There is a pseudogene for this gene on chromosome 12. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CRYBG1NM_001371242.2 linkuse as main transcriptc.*2846C>T 3_prime_UTR_variant 22/22 ENST00000633556.3 NP_001358171.1
RTN4IP1NM_032730.5 linkuse as main transcriptc.*584G>A 3_prime_UTR_variant 9/9 ENST00000369063.8 NP_116119.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RTN4IP1ENST00000369063.8 linkuse as main transcriptc.*584G>A 3_prime_UTR_variant 9/91 NM_032730.5 ENSP00000358059 P1Q8WWV3-1
CRYBG1ENST00000633556.3 linkuse as main transcriptc.*2846C>T 3_prime_UTR_variant 22/225 NM_001371242.2 ENSP00000488010 P1

Frequencies

GnomAD3 genomes
AF:
0.163
AC:
24744
AN:
151988
Hom.:
2474
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.282
Gnomad AMI
AF:
0.0877
Gnomad AMR
AF:
0.132
Gnomad ASJ
AF:
0.127
Gnomad EAS
AF:
0.142
Gnomad SAS
AF:
0.133
Gnomad FIN
AF:
0.123
Gnomad MID
AF:
0.188
Gnomad NFE
AF:
0.110
Gnomad OTH
AF:
0.164
GnomAD4 exome
AF:
0.107
AC:
29
AN:
272
Hom.:
1
Cov.:
0
AF XY:
0.109
AC XY:
17
AN XY:
156
show subpopulations
Gnomad4 AFR exome
AF:
0.250
Gnomad4 AMR exome
AF:
0.111
Gnomad4 EAS exome
AF:
0.100
Gnomad4 FIN exome
AF:
0.167
Gnomad4 NFE exome
AF:
0.0957
Gnomad4 OTH exome
AF:
0.500
GnomAD4 genome
AF:
0.163
AC:
24751
AN:
152106
Hom.:
2476
Cov.:
32
AF XY:
0.162
AC XY:
12022
AN XY:
74380
show subpopulations
Gnomad4 AFR
AF:
0.282
Gnomad4 AMR
AF:
0.131
Gnomad4 ASJ
AF:
0.127
Gnomad4 EAS
AF:
0.142
Gnomad4 SAS
AF:
0.133
Gnomad4 FIN
AF:
0.123
Gnomad4 NFE
AF:
0.110
Gnomad4 OTH
AF:
0.163
Alfa
AF:
0.123
Hom.:
2100
Bravo
AF:
0.169
Asia WGS
AF:
0.155
AC:
542
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
1.2
DANN
Benign
0.47

Splicing

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: rs9320182; hg19: chr6-107019287; API