dbSNP rs2780695: CRYBB2P1:n.574-6079G>A (chr22-25513844-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000509460.5(CRYBB2P1):n.574-6079G>A variant causes a intron 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
ENST00000509460.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.15

Publications

5 publications found

Variant links:

Genes affected

CRYBB2P1 (HGNC:):

CRYBB2P1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CRYBB2P1	ENST00000509460.5 link	n.574-6079G>A	intron_variant	Intron 4 of 5	3
CRYBB2P1	ENST00000686640.3 link	n.576-6838G>A	intron_variant	Intron 4 of 4
CRYBB2P1	ENST00000818131.1 link	n.673-6079G>A	intron_variant	Intron 5 of 7

Frequencies

GnomAD3 genomes

AF:

0.111

AC:

16745

AN:

151276

Hom.:

1445

Cov.:

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.:

AF XY:

0.116

AC XY:

8597

AN XY:

73928

show subpopulations

African (AFR)

AF:

0.0335

AC:

1381

AN:

41216

American (AMR)

AF:

0.194

AC:

2950

AN:

15210

Ashkenazi Jewish (ASJ)

AF:

0.156

AC:

540

AN:

3466

East Asian (EAS)

AF:

0.360

AC:

1855

AN:

5154

South Asian (SAS)

AF:

0.226

AC:

1082

AN:

4780

European-Finnish (FIN)

AF:

0.113

AC:

1182

AN:

10418

Middle Eastern (MID)

AF:

0.142

AC:

AN:

282

European-Non Finnish (NFE)

AF:

0.108

AC:

7315

AN:

67840

Other (OTH)

AF:

0.135

AC:

284

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

666

1331

1997

2662

3328

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

198

396

594

792

990

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.120

Hom.:

754

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

(source)

DANN

Benign

0.42

PhyloP100

1.1

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over