22-25525901-T-G

Variant names:

• chr22-25525901-T-G
• rs635361
• ENST00000818131.1:n.964+5168T>G

Variant summary

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

The ENST00000818131.1(CRYBB2P1):​n.964+5168T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 135,330 control chromosomes in the GnomAD database, including 27,010 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 0.65 (27010 hom., cov: 34)
• Consequence: CRYBB2P1 ENST00000818131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 3 publications found

Genes affected

CRYBB2P1 (HGNC:):

GRK3-AS1 (HGNC:55679): (GRK3 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000818131.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRYBB2P1	ENST00000818131.1		n.964+5168T>G		intron	N/A
	CRYBB2P1	ENST00000818132.1		n.295+5168T>G		intron	N/A
	CRYBB2P1	ENST00000818142.1		n.686+5168T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.653 AC: 88357 AN: 135214 Hom.: 26937 Cov.: 34

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.642

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.654 AC: 88486 AN: 135330 Hom.: 27010 Cov.: 34 AF XY: 0.657 AC XY: 43712 AN XY: 66508

African (AFR) AF: 0.804 AC: 32533 AN: 40442

American (AMR) AF: 0.687 AC: 9617 AN: 13994

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1682 AN: 2998

East Asian (EAS) AF: 0.890 AC: 4575 AN: 5140

South Asian (SAS) AF: 0.726 AC: 3327 AN: 4582

European-Finnish (FIN) AF: 0.583 AC: 5342 AN: 9168

Middle Eastern (MID) AF: 0.613 AC: 146 AN: 238

European-Non Finnish (NFE) AF: 0.528 AC: 29664 AN: 56152

Other (OTH) AF: 0.648 AC: 1221 AN: 1884

Alfa AF: 0.564 Hom.: 2352

Asia WGS AF: 0.782 AC: 2717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.44
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs635361; hg19: chr22-25921868;