rs7740539

chr6-106383791-T-C

Variant summary

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

The NM_001371242.2(CRYBG1):c.173+22710T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,132 control chromosomes in the GnomAD database, including 5,723 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 0.27 (5723 hom., cov: 32)
• Consequence: CRYBG1 NM_001371242.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.183

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=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRYBG1	NM_001371242.2	c.173+22710T>C		intron_variant		ENST00000633556.3
CRYBG1	XM_047418270.1	c.174-14370T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRYBG1	ENST00000633556.3	c.173+22710T>C		intron_variant		5	NM_001371242.2	P1

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40769 AN: 152014 Hom.: 5720 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.268 AC: 40786 AN: 152132 Hom.: 5723 Cov.: 32 AF XY: 0.274 AC XY: 20402 AN XY: 74362

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.264

Alfa AF: 0.293 Hom.: 8905

Bravo AF: 0.258

Asia WGS AF: 0.286 AC: 993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	12
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7740539; hg19: chr6-106831666;