Variant 6-106451351-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001371242.2(CRYBG1):c.174-343C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 165,756 control chromosomes in the GnomAD database, including 41,474 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 0.71 ( 37943 hom., cov: 32)

Exomes 𝑓: 0.72 ( 3531 hom. )

Consequence

CRYBG1
NM_001371242.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.618

Variant links:

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]

CRYBG1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CRYBG1	NM_001371242.2 linkuse as main transcript	c.174-343C>T		intron_variant		ENST00000633556.3	NP_001358171.1
CRYBG1	XM_047418270.1 linkuse as main transcript	c.252-343C>T		intron_variant			XP_047274226.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRYBG1	ENST00000633556.3 linkuse as main transcript	c.174-343C>T		intron_variant		5	NM_001371242.2	ENSP00000488010.2		A0A0J9YWL0

Frequencies

GnomAD3 genomes

AF:

0.706

AC:

107224

AN:

151920

Hom.:

37893

Cov.:

show subpopulations

Gnomad AFR

AF:

0.706

Gnomad AMI

AF:

0.805

Gnomad AMR

AF:

0.708

Gnomad ASJ

AF:

0.820

Gnomad EAS

AF:

0.658

Gnomad SAS

AF:

0.637

Gnomad FIN

AF:

0.646

Gnomad MID

AF:

0.775

Gnomad NFE

AF:

0.715

Gnomad OTH

AF:

0.719

GnomAD4 exome

AF:

0.715

AC:

9814

AN:

13718

Hom.:

3531

AF XY:

0.717

AC XY:

5029

AN XY:

7014

show subpopulations

Gnomad4 AFR exome

AF:

0.702

Gnomad4 AMR exome

AF:

0.733

Gnomad4 ASJ exome

AF:

0.836

Gnomad4 EAS exome

AF:

0.651

Gnomad4 SAS exome

AF:

0.643

Gnomad4 FIN exome

AF:

0.655

Gnomad4 NFE exome

AF:

0.719

Gnomad4 OTH exome

AF:

0.716

GnomAD4 genome

AF:

0.706

AC:

107329

AN:

152038

Hom.:

37943

Cov.:

AF XY:

0.705

AC XY:

52386

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.707

Gnomad4 AMR

AF:

0.709

Gnomad4 ASJ

AF:

0.820

Gnomad4 EAS

AF:

0.658

Gnomad4 SAS

AF:

0.638

Gnomad4 FIN

AF:

0.646

Gnomad4 NFE

AF:

0.715

Gnomad4 OTH

AF:

0.722

Alfa

AF:

0.717

Hom.:

84435

Bravo

AF:

0.713

Asia WGS

AF:

0.641

AC:

2227

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

6.5

DANN

Benign

0.62

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over