rs6568433

Positions:

• chr6-106381662-T-C
• chr6-106381662-T-G

Variant summary

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

The NM_001371242.2(CRYBG1):​c.173+20581T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 152,084 control chromosomes in the GnomAD database, including 17,831 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 0.48 (17831 hom., cov: 33)
• Consequence: CRYBG1 NM_001371242.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CRYBG1	NM_001371242.2	c.173+20581T>C		intron_variant		ENST00000633556.3	NP_001358171.1
CRYBG1	XM_047418270.1	c.174-16499T>C		intron_variant			XP_047274226.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRYBG1	ENST00000633556.3	c.173+20581T>C		intron_variant		5	NM_001371242.2	ENSP00000488010	P1

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72857 AN: 151966 Hom.: 17796 Cov.: 33

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.480 AC: 72949 AN: 152084 Hom.: 17831 Cov.: 33 AF XY: 0.483 AC XY: 35929 AN XY: 74352

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.482

Alfa AF: 0.447 Hom.: 35826

Bravo AF: 0.495

Asia WGS AF: 0.450 AC: 1562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.024
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6568433; hg19: chr6-106829537;