chr3-97887828-A-G

Position:

• chr3-97887828-A-G

Variant summary

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

The NM_153605.4(CRYBG3):​c.7290-513A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0937 in 152,222 control chromosomes in the GnomAD database, including 860 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 0.094 (860 hom., cov: 32)
• Consequence: CRYBG3 NM_153605.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.247

Genes affected

CRYBG3 (HGNC:34427): (crystallin beta-gamma domain containing 3) Enables protein kinase A binding activity. Predicted to be involved in lens development in camera-type eye and visual perception. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRYBG3	NM_153605.4	c.7290-513A>G		intron_variant		ENST00000389622.7
CRYBG3	XM_005247117.5	c.6417-513A>G		intron_variant
CRYBG3	XM_047447439.1	c.7290-513A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRYBG3	ENST00000389622.7	c.7290-513A>G		intron_variant		5	NM_153605.4	P1

Frequencies

GnomAD3 genomes AF: 0.0938 AC: 14269 AN: 152104 Hom.: 862 Cov.: 32

Gnomad AFR AF: 0.0246

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0877

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0933

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.0947

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

GnomAD4 genome AF: 0.0937 AC: 14261 AN: 152222 Hom.: 860 Cov.: 32 AF XY: 0.0925 AC XY: 6883 AN XY: 74426

Gnomad4 AFR AF: 0.0245

Gnomad4 AMR AF: 0.0874

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.0933

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.0942

Alfa AF: 0.123 Hom.: 1627

Bravo AF: 0.0891

Asia WGS AF: 0.111 AC: 383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	16
DANN	Benign	0.88

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12637414; hg19: chr3-97606672;