Variant chr22-25478613-A-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000609475.1(ENSG00000272977):n.2396A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 151,954 control chromosomes in the GnomAD database, including 7,438 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 0.22 ( 7438 hom., cov: 33)

Exomes 𝑓: 0.071 ( 0 hom. )

Consequence

ENST00000609475.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.194

Variant links:

Genes affected

(HGNC:):

links:

CRYBB2P1 (HGNC:2399): (crystallin beta B2 pseudogene 1)

CRYBB2P1 links:

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=-0.78).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124905094	XR_007068036.1 linkuse as main transcript	n.4457A>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
	ENST00000609475.1 linkuse as main transcript	n.2396A>C	non_coding_transcript_exon_variant	1/1
CRYBB2P1	ENST00000354451.6 linkuse as main transcript	n.366+19098A>C	intron_variant, non_coding_transcript_variant		1
CRYBB2P1	ENST00000686640.2 linkuse as main transcript	n.573+19098A>C	intron_variant, non_coding_transcript_variant
CRYBB2P1	ENST00000509460.4 linkuse as main transcript	n.568+19098A>C	intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.224

AC:

34027

AN:

151822

Hom.:

7396

Cov.:

show subpopulations

Gnomad AFR

AF:

0.568

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.175

Gnomad ASJ

AF:

0.0701

Gnomad EAS

AF:

0.0921

Gnomad SAS

AF:

0.161

Gnomad FIN

AF:

0.0665

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.0777

Gnomad OTH

AF:

0.193

GnomAD4 exome

AF:

0.0714

AC:

AN:

Hom.:

Cov.:

AF XY:

0.100

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.00

GnomAD4 genome

AF:

0.225

AC:

34138

AN:

151940

Hom.:

7438

Cov.:

AF XY:

0.222

AC XY:

16497

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.568

Gnomad4 AMR

AF:

0.176

Gnomad4 ASJ

AF:

0.0701

Gnomad4 EAS

AF:

0.0923

Gnomad4 SAS

AF:

0.161

Gnomad4 FIN

AF:

0.0665

Gnomad4 NFE

AF:

0.0777

Gnomad4 OTH

AF:

0.196

Alfa

AF:

0.125

Hom.:

1065

Bravo

AF:

0.249

Asia WGS

AF:

0.187

AC:

650

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

8.8

DANN

Benign

0.83

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over