rs2780695

Variant names:

• chr22-25513844-G-A
• rs2780695
• ENST00000509460.4:n.569-6079G>A

Variant summary

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

The ENST00000509460.4(CRYBB2P1):​n.569-6079G>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 ENST00000509460.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

Genes affected

CRYBB2P1 (HGNC:):

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRYBB2P1	ENST00000509460.4	n.569-6079G>A		intron_variant	Intron 4 of 5	3
CRYBB2P1	ENST00000686640.2	n.574-6838G>A		intron_variant	Intron 4 of 4

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;