rs9320174

Positions:

• chr6-106537533-A-G

Variant summary

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

The NM_001371242.2(CRYBG1):​c.4719-1870A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,150 control chromosomes in the GnomAD database, including 7,200 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 0.30 (7200 hom., cov: 32)
• Consequence: CRYBG1 NM_001371242.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.310

Genes affected

CRYBG1 (HGNC:356): (crystallin beta-gamma domain containing 1) Predicted to enable carbohydrate binding activity. [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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CRYBG1	NM_001371242.2	c.4719-1870A>G		intron_variant		ENST00000633556.3	NP_001358171.1
CRYBG1	NM_001624.4	c.3495-1870A>G		intron_variant			NP_001615.2
CRYBG1	XM_047418270.1	c.4797-1870A>G		intron_variant			XP_047274226.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRYBG1	ENST00000633556.3	c.4719-1870A>G		intron_variant		5	NM_001371242.2	ENSP00000488010	P1

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45686 AN: 152032 Hom.: 7184 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.0519

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.301 AC: 45736 AN: 152150 Hom.: 7200 Cov.: 32 AF XY: 0.299 AC XY: 22222 AN XY: 74366

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.0519

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.293

Alfa AF: 0.298 Hom.: 1199

Bravo AF: 0.297

Asia WGS AF: 0.229 AC: 793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.6
DANN	Benign	0.63

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: rs9320174; hg19: chr6-106985408;