dbSNP rs748806: GNB1L:c.732+1788G>A (chr22-19800213-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_053004.3(GNB1L):c.732+1788G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,260 control chromosomes in the GnomAD database, including 1,770 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 0.12 ( 1770 hom., cov: 33)

Consequence

GNB1L
NM_053004.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0930

Publications

15 publications found

Variant links:

Genes affected

GNB1L (HGNC:4397): (G protein subunit beta 1 like) This gene encodes a G-protein beta-subunit-like polypeptide which is a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. This protein contains 6 WD repeats and is highly expressed in the heart. The gene maps to the region on chromosome 22q11, which is deleted in DiGeorge syndrome, trisomic in derivative 22 syndrome and tetrasomic in cat-eye syndrome. Therefore, this gene may contribute to the etiology of those disorders. Transcripts from this gene share exons with some transcripts from the C22orf29 gene. [provided by RefSeq, Jul 2008]

GNB1L links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.31).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GNB1L	NM_053004.3 link	c.732+1788G>A		intron_variant	Intron 7 of 7	ENST00000329517.11	NP_443730.1	Q9BYB4-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
GNB1L	ENST00000329517.11 link	c.732+1788G>A	intron_variant	Intron 7 of 7	1	NM_053004.3	ENSP00000331313.6	Q9BYB4-1
GNB1L	ENST00000403325.5 link	c.732+1788G>A	intron_variant	Intron 6 of 6	1		ENSP00000385154.1	Q9BYB4-1
GNB1L	ENST00000405009.5 link	c.630+1890G>A	intron_variant	Intron 7 of 7	1		ENSP00000384626.1	Q9BYB4-2
GNB1L	ENST00000460402.5 link	n.700+1788G>A	intron_variant	Intron 5 of 5	3

Frequencies

GnomAD3 genomes

AF:

0.123

AC:

18739

AN:

152142

Hom.:

1767

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0546

Gnomad AMI

AF:

0.219

Gnomad AMR

AF:

0.221

Gnomad ASJ

AF:

0.213

Gnomad EAS

AF:

0.478

Gnomad SAS

AF:

0.219

Gnomad FIN

AF:

0.0591

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.113

Gnomad OTH

AF:

0.128

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.123

AC:

18751

AN:

152260

Hom.:

1770

Cov.:

AF XY:

0.128

AC XY:

9563

AN XY:

74456

show subpopulations

African (AFR)

AF:

0.0548

AC:

2279

AN:

41562

American (AMR)

AF:

0.222

AC:

3389

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.213

AC:

739

AN:

3472

East Asian (EAS)

AF:

0.477

AC:

2459

AN:

5150

South Asian (SAS)

AF:

0.219

AC:

1057

AN:

4828

European-Finnish (FIN)

AF:

0.0591

AC:

628

AN:

10624

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.113

AC:

7695

AN:

68010

Other (OTH)

AF:

0.125

AC:

265

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

820

1640

2461

3281

4101

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

212

424

636

848

1060

<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:

0.127

Hom.:

1152

Bravo

AF:

0.132

Asia WGS

AF:

0.292

AC:

1014

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.31

CADD

Benign

(source)

DANN

Benign

0.86

PhyloP100

0.093

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over