dbSNP rs7143583: RRAGAP1-AS1:n.53-14090C>T (chr14-44845780-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000715832.1(RRAGAP1-AS1):n.53-14090C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,098 control chromosomes in the GnomAD database, including 1,860 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 0.15 ( 1860 hom., cov: 32)

Consequence

RRAGAP1-AS1
ENST00000715832.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.132

Publications

6 publications found

Variant links:

Genes affected

RRAGAP1-AS1 (HGNC:55445): (RRAGAP1 antisense RNA 1)

RRAGAP1-AS1 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=-0.51).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
RRAGAP1-AS1	ENST00000715832.1 link	n.53-14090C>T	intron_variant	Intron 1 of 7
RRAGAP1-AS1	ENST00000715833.1 link	n.366-14090C>T	intron_variant	Intron 3 of 7
RRAGAP1-AS1	ENST00000780005.1 link	n.366-14090C>T	intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes

AF:

0.147

AC:

22288

AN:

151980

Hom.:

1859

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0748

Gnomad AMI

AF:

0.149

Gnomad AMR

AF:

0.184

Gnomad ASJ

AF:

0.175

Gnomad EAS

AF:

0.106

Gnomad SAS

AF:

0.204

Gnomad FIN

AF:

0.137

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.179

Gnomad OTH

AF:

0.181

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

GnomAD4 genome

AF:

0.147

AC:

22313

AN:

152098

Hom.:

1860

Cov.:

AF XY:

0.146

AC XY:

10895

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.0747

AC:

3100

AN:

41492

American (AMR)

AF:

0.184

AC:

2815

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.175

AC:

606

AN:

3470

East Asian (EAS)

AF:

0.106

AC:

547

AN:

5174

South Asian (SAS)

AF:

0.206

AC:

990

AN:

4808

European-Finnish (FIN)

AF:

0.137

AC:

1451

AN:

10588

Middle Eastern (MID)

AF:

0.276

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.179

AC:

12198

AN:

67984

Other (OTH)

AF:

0.185

AC:

389

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

956

1913

2869

3826

4782

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

260

520

780

1040

1300

<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:

0.174

Hom.:

8301

Bravo

AF:

0.149

Asia WGS

AF:

0.154

AC:

538

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

7.0

(source)

DANN

Benign

0.52

PhyloP100

-0.13

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