rs1422871

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000509018.6(RAPGEF6):​c.70-2095C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 152,116 control chromosomes in the GnomAD database, including 46,622 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 0.78 ( 46622 hom., cov: 32)

Consequence

RAPGEF6
ENST00000509018.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.173
Variant links:
Genes affected
RAPGEF6 (HGNC:20655): (Rap guanine nucleotide exchange factor 6) Enables several functions, including GTP-dependent protein binding activity; guanyl-nucleotide exchange factor activity; and phosphatidic acid binding activity. Involved in microvillus assembly; positive regulation of GTPase activity; and protein localization to plasma membrane. Located in several cellular components, including apical plasma membrane; centrosome; and endocytic vesicle. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RAPGEF6NM_016340.6 linkuse as main transcriptc.70-2095C>T intron_variant ENST00000509018.6 NP_057424.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RAPGEF6ENST00000509018.6 linkuse as main transcriptc.70-2095C>T intron_variant 1 NM_016340.6 ENSP00000421684 P4Q8TEU7-1

Frequencies

GnomAD3 genomes
AF:
0.780
AC:
118518
AN:
151998
Hom.:
46591
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.836
Gnomad AMI
AF:
0.733
Gnomad AMR
AF:
0.753
Gnomad ASJ
AF:
0.723
Gnomad EAS
AF:
0.475
Gnomad SAS
AF:
0.752
Gnomad FIN
AF:
0.639
Gnomad MID
AF:
0.826
Gnomad NFE
AF:
0.801
Gnomad OTH
AF:
0.791
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.780
AC:
118602
AN:
152116
Hom.:
46622
Cov.:
32
AF XY:
0.771
AC XY:
57314
AN XY:
74352
show subpopulations
Gnomad4 AFR
AF:
0.836
Gnomad4 AMR
AF:
0.752
Gnomad4 ASJ
AF:
0.723
Gnomad4 EAS
AF:
0.475
Gnomad4 SAS
AF:
0.752
Gnomad4 FIN
AF:
0.639
Gnomad4 NFE
AF:
0.801
Gnomad4 OTH
AF:
0.791
Alfa
AF:
0.768
Hom.:
6953
Bravo
AF:
0.788
Asia WGS
AF:
0.617
AC:
2146
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
1.5
DANN
Benign
0.39

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1422871; hg19: chr5-130942481; API