dbSNP rs7300713: RERGL:n.62-42433A>G (chr12-18131389-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000540148.5(RERGL):n.62-42433A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,124 control chromosomes in the GnomAD database, including 1,073 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 ( 1073 hom., cov: 32)

Consequence

RERGL
ENST00000540148.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.307

Publications

3 publications found

Variant links:

Genes affected

RERGL (HGNC:26213): (RERG like) Predicted to enable G protein activity and GTP binding activity. [provided by Alliance of Genome Resources, Apr 2022]

RERGL 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=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RERGL	ENST00000540148.5 link	n.62-42433A>G		intron_variant	Intron 1 of 4	3
RERGL	ENST00000541632.1 link	n.341+9403A>G		intron_variant	Intron 4 of 7	3

Frequencies

GnomAD3 genomes

AF:

0.115

AC:

17527

AN:

152006

Hom.:

1070

Cov.:

show subpopulations

Gnomad AFR

AF:

0.123

Gnomad AMI

AF:

0.107

Gnomad AMR

AF:

0.108

Gnomad ASJ

AF:

0.159

Gnomad EAS

AF:

0.00231

Gnomad SAS

AF:

0.112

Gnomad FIN

AF:

0.0899

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.123

Gnomad OTH

AF:

0.112

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

GnomAD4 genome

AF:

0.115

AC:

17545

AN:

152124

Hom.:

1073

Cov.:

AF XY:

0.113

AC XY:

8410

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.123

AC:

5093

AN:

41526

American (AMR)

AF:

0.108

AC:

1644

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.159

AC:

553

AN:

3470

East Asian (EAS)

AF:

0.00232

AC:

AN:

5180

South Asian (SAS)

AF:

0.113

AC:

543

AN:

4816

European-Finnish (FIN)

AF:

0.0899

AC:

952

AN:

10592

Middle Eastern (MID)

AF:

0.170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.123

AC:

8370

AN:

67966

Other (OTH)

AF:

0.110

AC:

231

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

808

1616

2425

3233

4041

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

208

416

624

832

1040

<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:

0.112

Hom.:

383

Bravo

AF:

0.117

Asia WGS

AF:

0.0560

AC:

195

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.0

(source)

DANN

Benign

0.65

PhyloP100

0.31

Splicing

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