Genetic Variant NM_001039775.4:c.4737+93G>A (chr1-26324059-C-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001039775.4(CRYBG2):c.4737+93G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000818 in 1,221,852 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 31)

Exomes 𝑓: 8.2e-7 ( 0 hom. )

Consequence

CRYBG2
NM_001039775.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0660

Publications

0 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: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CRYBG2	NM_001039775.4 link	c.4737+93G>A	intron_variant	Intron 18 of 19	ENST00000308182.10	NP_001034864.2	Q8N1P7Q9NWG5
CRYBG2	XM_011541673.3 link	c.4908+93G>A	intron_variant	Intron 18 of 19		XP_011539975.1
CRYBG2	XM_005245918.3 link	c.4737+93G>A	intron_variant	Intron 18 of 19		XP_005245975.1	Q8N1P7
CRYBG2	XM_011541672.2 link	c.4701+93G>A	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>A	intron_variant	Intron 18 of 19	5	NM_001039775.4	ENSP00000310435.6	Q8N1P7
CRYBG2	ENST00000475866.3 link	c.5709+93G>A	intron_variant	Intron 20 of 21	4		ENSP00000428746.2	E7ET48
CRYBG2	ENST00000374208.1 link	n.215+93G>A	intron_variant	Intron 2 of 3	5
CRYBG2	ENST00000374211.5 link	n.351+93G>A	intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

8.18e-7

AC:

AN:

1221852

Hom.:

AF XY:

0.00

AC XY:

AN XY:

606638

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

28174

American (AMR)

AF:

0.0000277

AC:

AN:

36102

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

20120

East Asian (EAS)

AF:

0.00

AC:

AN:

37792

South Asian (SAS)

AF:

0.00

AC:

AN:

71566

European-Finnish (FIN)

AF:

0.00

AC:

AN:

43036

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5068

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

928448

Other (OTH)

AF:

0.00

AC:

AN:

51546

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

5.6

(source)

DANN

Benign

0.76

PhyloP100

0.066

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over