dbSNP rs6423498: CRYBB2P1:n.266T>A (chr22-25457401-T-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The ENST00000354451.6(CRYBB2P1):n.266T>A variant causes a splice region, non coding transcript exon change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Consequence

CRYBB2P1
ENST00000354451.6 splice_region, non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.12

Variant links:

Genes affected

CRYBB2P1 (HGNC:):

CRYBB2P1 links:

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

CRYBB2P1 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CRYBB2P1	NR_033733.1 link	n.589T>A		splice_region_variant, non_coding_transcript_exon_variant	Exon 4 of 6
CRYBB2P1	NR_033734.1 link	n.470T>A		splice_region_variant, non_coding_transcript_exon_variant	Exon 3 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CRYBB2P1	ENST00000354451.6 link	n.266T>A	splice_region_variant, non_coding_transcript_exon_variant	Exon 2 of 6	1
CRYBB2P1	ENST00000382734.10 link	n.477T>A	splice_region_variant, non_coding_transcript_exon_variant	Exon 3 of 5	1
CRYBB2P1	ENST00000415709.7 link	n.272T>A	splice_region_variant, non_coding_transcript_exon_variant	Exon 2 of 3	6

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

DANN

Benign

0.69

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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