2-208124313-A-G

Position:

chr2-208124313-A-G

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_006891.4(CRYGD):c.51T>C(p.Tyr17=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 1,608,444 control chromosomes in the GnomAD database, including 255,625 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.60 ( 28162 hom., cov: 33)

Exomes 𝑓: 0.56 ( 227463 hom. )

Consequence

CRYGD
NM_006891.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 0.446

Variant links:

Genes affected

CRYGD (HGNC:2411): (crystallin gamma D) Crystallins are separated into two classes: taxon-specific, or enzyme, and ubiquitous. The latter class constitutes the major proteins of vertebrate eye lens and maintains the transparency and refractive index of the lens. Since lens central fiber cells lose their nuclei during development, these crystallins are made and then retained throughout life, making them extremely stable proteins. Mammalian lens crystallins are divided into alpha, beta, and gamma families; beta and gamma crystallins are also considered as a superfamily. Alpha and beta families are further divided into acidic and basic groups. Seven protein regions exist in crystallins: four homologous motifs, a connecting peptide, and N- and C-terminal extensions. Gamma-crystallins are a homogeneous group of highly symmetrical, monomeric proteins typically lacking connecting peptides and terminal extensions. They are differentially regulated after early development. Four gamma-crystallin genes (gamma-A through gamma-D) and three pseudogenes (gamma-E, gamma-F, gamma-G) are tandemly organized in a genomic segment as a gene cluster. Whether due to aging or mutations in specific genes, gamma-crystallins have been involved in cataract formation. [provided by RefSeq, Jul 2008]

CRYGD links:

LOC100507443 (HGNC:):

LOC100507443 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BP6

Variant 2-208124313-A-G is Benign according to our data. Variant chr2-208124313-A-G is described in ClinVar as [Benign]. Clinvar id is 260062.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-208124313-A-G is described in Lovd as [Benign]. Variant chr2-208124313-A-G is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=0.446 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CRYGD	NM_006891.4 linkuse as main transcript	c.51T>C	p.Tyr17=	synonymous_variant	2/3	ENST00000264376.5	NP_008822.2
LOC100507443	NR_038437.1 linkuse as main transcript	n.97+5088A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRYGD	ENST00000264376.5 linkuse as main transcript	c.51T>C	p.Tyr17=	synonymous_variant	2/3	1	NM_006891.4	ENSP00000264376	P1

Frequencies

GnomAD3 genomes

AF:

0.601

AC:

91350

AN:

152014

Hom.:

28117

Cov.:

show subpopulations

Gnomad AFR

AF:

0.723

Gnomad AMI

AF:

0.341

Gnomad AMR

AF:

0.546

Gnomad ASJ

AF:

0.704

Gnomad EAS

AF:

0.651

Gnomad SAS

AF:

0.743

Gnomad FIN

AF:

0.536

Gnomad MID

AF:

0.690

Gnomad NFE

AF:

0.532

Gnomad OTH

AF:

0.619

GnomAD3 exomes

AF:

0.584

AC:

138623

AN:

237444

Hom.:

40915

AF XY:

0.591

AC XY:

76354

AN XY:

129272

show subpopulations

Gnomad AFR exome

AF:

0.719

Gnomad AMR exome

AF:

0.504

Gnomad ASJ exome

AF:

0.702

Gnomad EAS exome

AF:

0.664

Gnomad SAS exome

AF:

0.733

Gnomad FIN exome

AF:

0.530

Gnomad NFE exome

AF:

0.535

Gnomad OTH exome

AF:

0.575

GnomAD4 exome

AF:

0.555

AC:

808610

AN:

1456312

Hom.:

227463

Cov.:

AF XY:

0.561

AC XY:

405857

AN XY:

724068

show subpopulations

Gnomad4 AFR exome

AF:

0.729

Gnomad4 AMR exome

AF:

0.505

Gnomad4 ASJ exome

AF:

0.705

Gnomad4 EAS exome

AF:

0.652

Gnomad4 SAS exome

AF:

0.733

Gnomad4 FIN exome

AF:

0.528

Gnomad4 NFE exome

AF:

0.530

Gnomad4 OTH exome

AF:

0.588

GnomAD4 genome

AF:

0.601

AC:

91445

AN:

152132

Hom.:

28162

Cov.:

AF XY:

0.604

AC XY:

44932

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.724

Gnomad4 AMR

AF:

0.546

Gnomad4 ASJ

AF:

0.704

Gnomad4 EAS

AF:

0.651

Gnomad4 SAS

AF:

0.741

Gnomad4 FIN

AF:

0.536

Gnomad4 NFE

AF:

0.532

Gnomad4 OTH

AF:

0.622

Alfa

AF:

0.573

Hom.:

11751

Bravo

AF:

0.604

Asia WGS

AF:

0.708

AC:

2461

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

Cataract 4 multiple types

Benign:2

Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 30, 2021	- -

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 24, 2018	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Aculeiform cataract

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 27, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

6.2

DANN

Benign

0.67

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over