rs2780695

Positions:

• chr22-25513844-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

Genes affected

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

ACMG classification

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
CRYBB2P1	ENST00000686640.2	n.574-6838G>A		intron_variant, non_coding_transcript_variant
CRYBB2P1	ENST00000509460.4	n.569-6079G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16745 AN: 151276 Hom.: 1445 Cov.: 32

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

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

Other links and lift over

dbSNP: rs2780695; hg19: chr22-25909811;