6-106472030-G-A

Position:

• chr6-106472030-G-A

Variant summary

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

The NM_001371242.2(CRYBG1):​c.312+20198G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0835 in 152,180 control chromosomes in the GnomAD database, including 691 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 0.084 (691 hom., cov: 32)
• Consequence: CRYBG1 NM_001371242.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.734

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CRYBG1	NM_001371242.2	c.312+20198G>A		intron_variant		ENST00000633556.3	NP_001358171.1
CRYBG1	XM_047418270.1	c.390+20198G>A		intron_variant			XP_047274226.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRYBG1	ENST00000633556.3	c.312+20198G>A		intron_variant		5	NM_001371242.2	ENSP00000488010	P1
CRYBG1	ENST00000651520.1	c.153+10090G>A		intron_variant				ENSP00000499126

Frequencies

GnomAD3 genomes AF: 0.0836 AC: 12707 AN: 152062 Hom.: 691 Cov.: 32

Gnomad AFR AF: 0.0953

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.0236

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0551

Gnomad OTH AF: 0.0794

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

GnomAD4 genome AF: 0.0835 AC: 12713 AN: 152180 Hom.: 691 Cov.: 32 AF XY: 0.0855 AC XY: 6366 AN XY: 74416

Gnomad4 AFR AF: 0.0951

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.0519

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.0238

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.0551

Gnomad4 OTH AF: 0.0781

Alfa AF: 0.0699 Hom.: 80

Bravo AF: 0.0906

Asia WGS AF: 0.102 AC: 355 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	7.9
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7356791; hg19: chr6-106919905;