22-25513844-G-A

Variant names:

• chr22-25513844-G-A
• rs2780695
• ENST00000509460.5:n.574-6079G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 5 publications found

Genes affected

CRYBB2P1 (HGNC:):

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509460.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRYBB2P1	ENST00000509460.5	TSL:3	n.574-6079G>A		intron	N/A
	CRYBB2P1	ENST00000686640.3		n.576-6838G>A		intron	N/A
	CRYBB2P1	ENST00000818131.1		n.673-6079G>A		intron	N/A

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

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: 40 AN: 282

European-Non Finnish (NFE) AF: 0.108 AC: 7315 AN: 67840

Other (OTH) AF: 0.135 AC: 284 AN: 2100

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.0
DANN	Benign	0.42
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2780695; hg19: chr22-25909811;