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. Variant has been reported in ClinVar as (no stars).

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:

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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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001039775.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRYBG2	NM_001039775.4	MANE Select	c.4737+93G>T		intron	N/A	NP_001034864.2	Q8N1P7

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CRYBG2	ENST00000308182.10	TSL:5 MANE Select	c.4737+93G>T	intron	N/A	ENSP00000310435.6	Q8N1P7
CRYBG2	ENST00000475866.3	TSL:4	c.5709+93G>T	intron	N/A	ENSP00000428746.2	E7ET48
CRYBG2	ENST00000374208.1	TSL:5	n.215+93G>T	intron	N/A

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over