dbSNP rs11247915: CRYBG2:c.4737+93G>T (chr1-26324059-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001039775.4(CRYBG2):c.4737+93G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 1,370,862 control chromosomes in the GnomAD database, including 166,416 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 0.45 ( 16250 hom., cov: 31)

Exomes 𝑓: 0.48 ( 150166 hom. )

Consequence

CRYBG2
NM_001039775.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0660

Publications

10 publications found

Variant links:

Genes affected

CRYBG2 (HGNC:17295): (crystallin beta-gamma domain containing 2) Predicted to enable carbohydrate binding activity. [provided by Alliance of Genome Resources, Apr 2022]

CRYBG2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CRYBG2	NM_001039775.4 link	c.4737+93G>T	intron_variant	Intron 18 of 19	ENST00000308182.10	NP_001034864.2	Q8N1P7Q9NWG5
CRYBG2	XM_011541673.3 link	c.4908+93G>T	intron_variant	Intron 18 of 19		XP_011539975.1
CRYBG2	XM_005245918.3 link	c.4737+93G>T	intron_variant	Intron 18 of 19		XP_005245975.1	Q8N1P7
CRYBG2	XM_011541672.2 link	c.4701+93G>T	intron_variant	Intron 17 of 18		XP_011539974.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CRYBG2	ENST00000308182.10 link	c.4737+93G>T	intron_variant	Intron 18 of 19	5	NM_001039775.4	ENSP00000310435.6	Q8N1P7
CRYBG2	ENST00000475866.3 link	c.5709+93G>T	intron_variant	Intron 20 of 21	4		ENSP00000428746.2	E7ET48
CRYBG2	ENST00000374208.1 link	n.215+93G>T	intron_variant	Intron 2 of 3	5
CRYBG2	ENST00000374211.5 link	n.351+93G>T	intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.449

AC:

68152

AN:

151696

Hom.:

16255

Cov.:

show subpopulations

Gnomad AFR

AF:

0.414

Gnomad AMI

AF:

0.601

Gnomad AMR

AF:

0.342

Gnomad ASJ

AF:

0.519

Gnomad EAS

AF:

0.0609

Gnomad SAS

AF:

0.273

Gnomad FIN

AF:

0.508

Gnomad MID

AF:

0.528

Gnomad NFE

AF:

0.522

Gnomad OTH

AF:

0.436

GnomAD4 exome

AF:

0.483

AC:

588371

AN:

1219048

Hom.:

150166

AF XY:

0.478

AC XY:

289383

AN XY:

605354

show subpopulations

African (AFR)

AF:

0.414

AC:

11633

AN:

28102

American (AMR)

AF:

0.235

AC:

8460

AN:

36070

Ashkenazi Jewish (ASJ)

AF:

0.524

AC:

10515

AN:

20074

East Asian (EAS)

AF:

0.0495

AC:

1872

AN:

37782

South Asian (SAS)

AF:

0.291

AC:

20814

AN:

71484

European-Finnish (FIN)

AF:

0.503

AC:

21597

AN:

42930

Middle Eastern (MID)

AF:

0.467

AC:

2364

AN:

5064

European-Non Finnish (NFE)

AF:

0.526

AC:

487434

AN:

926116

Other (OTH)

AF:

0.461

AC:

23682

AN:

51426

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

13682

27363

41045

54726

68408

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13406

26812

40218

53624

67030

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.449

AC:

68166

AN:

151814

Hom.:

16250

Cov.:

AF XY:

0.439

AC XY:

32586

AN XY:

74204

show subpopulations

African (AFR)

AF:

0.414

AC:

17130

AN:

41360

American (AMR)

AF:

0.341

AC:

5199

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.519

AC:

1800

AN:

3468

East Asian (EAS)

AF:

0.0609

AC:

315

AN:

5176

South Asian (SAS)

AF:

0.272

AC:

1311

AN:

4818

European-Finnish (FIN)

AF:

0.508

AC:

5352

AN:

10542

Middle Eastern (MID)

AF:

0.517

AC:

152

AN:

294

European-Non Finnish (NFE)

AF:

0.522

AC:

35450

AN:

67894

Other (OTH)

AF:

0.433

AC:

910

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1797

3594

5392

7189

8986

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

618

1236

1854

2472

3090

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.460

Hom.:

12536

Bravo

AF:

0.436

Asia WGS

AF:

0.199

AC:

691

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

5.5

(source)

DANN

Benign

0.81

PhyloP100

0.066

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over