19-55762699-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001145014.2(RFPL4A):​c.388C>T​(p.Gln130*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000431 in 150,654 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00043 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000047 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

RFPL4A
NM_001145014.2 stop_gained

Scores

1
6

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.63
Variant links:
Genes affected
RFPL4A (HGNC:16449): (ret finger protein like 4A) Predicted to enable ubiquitin-protein transferase activity. Predicted to be involved in positive regulation of transcription, DNA-templated. Predicted to be located in nucleus. Predicted to be active in chromatin and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RFPL4ANM_001145014.2 linkc.388C>T p.Gln130* stop_gained Exon 3 of 3 ENST00000434937.3 NP_001138486.1 A6NLU0
RFPL4AXM_011526915.4 linkc.559C>T p.Gln187* stop_gained Exon 4 of 4 XP_011525217.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RFPL4AENST00000434937.3 linkc.388C>T p.Gln130* stop_gained Exon 3 of 3 5 NM_001145014.2 ENSP00000392936.2 A6NLU0

Frequencies

GnomAD3 genomes
AF:
0.000432
AC:
65
AN:
150542
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000969
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00100
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000419
Gnomad FIN
AF:
0.0000945
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000612
Gnomad OTH
AF:
0.000974
GnomAD3 exomes
AF:
0.0000579
AC:
9
AN:
155560
Hom.:
0
AF XY:
0.0000364
AC XY:
3
AN XY:
82478
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000813
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000117
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0000468
AC:
65
AN:
1389878
Hom.:
0
Cov.:
71
AF XY:
0.0000467
AC XY:
32
AN XY:
685544
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000565
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000203
Gnomad4 NFE exome
AF:
0.0000532
Gnomad4 OTH exome
AF:
0.0000695
GnomAD4 genome
AF:
0.000431
AC:
65
AN:
150654
Hom.:
0
Cov.:
33
AF XY:
0.000448
AC XY:
33
AN XY:
73698
show subpopulations
Gnomad4 AFR
AF:
0.0000967
Gnomad4 AMR
AF:
0.000999
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000419
Gnomad4 FIN
AF:
0.0000945
Gnomad4 NFE
AF:
0.000612
Gnomad4 OTH
AF:
0.000963
Alfa
AF:
0.000514
Hom.:
0
ExAC
AF:
0.000468
AC:
15

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
0.095
D
BayesDel_noAF
Benign
-0.10
CADD
Benign
22
DANN
Benign
0.95
Eigen
Benign
-0.32
Eigen_PC
Benign
-0.77
FATHMM_MKL
Benign
0.019
N
Vest4
0.034
GERP RS
-3.1

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: rs200829886; hg19: chr19-56274065; API