rs2780695

Variant summary

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

The ENST00000686640.2(CRYBB2P1):​n.574-6838G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 151,374 control chromosomes in the GnomAD database, including 1,454 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 0.11 ( 1454 hom., cov: 32)

Consequence

CRYBB2P1
ENST00000686640.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.15
Variant links:
Genes affected
CRYBB2P1 (HGNC:2399): (crystallin beta B2 pseudogene 1)

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=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CRYBB2P1ENST00000686640.2 linkuse as main transcriptn.574-6838G>A intron_variant, non_coding_transcript_variant
CRYBB2P1ENST00000509460.4 linkuse as main transcriptn.569-6079G>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.111
AC:
16745
AN:
151276
Hom.:
1445
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0335
Gnomad AMI
AF:
0.154
Gnomad AMR
AF:
0.193
Gnomad ASJ
AF:
0.156
Gnomad EAS
AF:
0.359
Gnomad SAS
AF:
0.226
Gnomad FIN
AF:
0.113
Gnomad MID
AF:
0.144
Gnomad NFE
AF:
0.108
Gnomad OTH
AF:
0.131
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.111
AC:
16769
AN:
151374
Hom.:
1454
Cov.:
32
AF XY:
0.116
AC XY:
8597
AN XY:
73928
show subpopulations
Gnomad4 AFR
AF:
0.0335
Gnomad4 AMR
AF:
0.194
Gnomad4 ASJ
AF:
0.156
Gnomad4 EAS
AF:
0.360
Gnomad4 SAS
AF:
0.226
Gnomad4 FIN
AF:
0.113
Gnomad4 NFE
AF:
0.108
Gnomad4 OTH
AF:
0.135
Alfa
AF:
0.121
Hom.:
713
Bravo
AF:
0.116
Asia WGS
AF:
0.275
AC:
956
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
5.0
DANN
Benign
0.42

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: rs2780695; hg19: chr22-25909811; API