rs12160908

Variant names:

• chr22-25532653-C-T
• rs12160908
• ENST00000818131.1:n.965-7873C>T

Variant summary

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

The ENST00000818131.1(CRYBB2P1):​n.965-7873C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 151,878 control chromosomes in the GnomAD database, including 1,124 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 0.12 (1124 hom., cov: 31)
• Consequence: CRYBB2P1 ENST00000818131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46
• Publications: 8 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=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.127 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	ENST00000818131.1	n.965-7873C>T		intron_variant	Intron 7 of 7
CRYBB2P1	ENST00000818132.1	n.296-7873C>T		intron_variant	Intron 4 of 4
CRYBB2P1	ENST00000818142.1	n.687-7873C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18027 AN: 151762 Hom.: 1120 Cov.: 31

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.0984

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.119 AC: 18052 AN: 151878 Hom.: 1124 Cov.: 31 AF XY: 0.118 AC XY: 8727 AN XY: 74260

African (AFR) AF: 0.118 AC: 4868 AN: 41412

American (AMR) AF: 0.118 AC: 1798 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 471 AN: 3466

East Asian (EAS) AF: 0.00271 AC: 14 AN: 5170

South Asian (SAS) AF: 0.0985 AC: 473 AN: 4804

European-Finnish (FIN) AF: 0.128 AC: 1355 AN: 10550

Middle Eastern (MID) AF: 0.0822 AC: 24 AN: 292

European-Non Finnish (NFE) AF: 0.129 AC: 8787 AN: 67910

Other (OTH) AF: 0.115 AC: 243 AN: 2110

Alfa AF: 0.126 Hom.: 1673

Bravo AF: 0.117

Asia WGS AF: 0.0490 AC: 168 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.46
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs12160908; hg19: chr22-25928620;