rs1054493594

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_005262.3(GFER):​c.42C>A​(p.Asn14Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000135 in 1,478,450 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 7.5e-7 ( 0 hom. )

Consequence

GFER
NM_005262.3 missense

Scores

1
18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.91
Variant links:
Genes affected
GFER (HGNC:4236): (growth factor, augmenter of liver regeneration) The hepatotrophic factor designated augmenter of liver regeneration (ALR) is thought to be one of the factors responsible for the extraordinary regenerative capacity of mammalian liver. It has also been called hepatic regenerative stimulation substance (HSS). The gene resides on chromosome 16 in the interval containing the locus for polycystic kidney disease (PKD1). The putative gene product is 42% similar to the scERV1 protein of yeast. The yeast scERV1 gene had been found to be essential for oxidative phosphorylation, the maintenance of mitochondrial genomes, and the cell division cycle. The human gene is both the structural and functional homolog of the yeast scERV1 gene. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.13949892).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GFERNM_005262.3 linkc.42C>A p.Asn14Lys missense_variant Exon 1 of 3 ENST00000248114.7 NP_005253.3 P55789-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GFERENST00000248114.7 linkc.42C>A p.Asn14Lys missense_variant Exon 1 of 3 1 NM_005262.3 ENSP00000248114.6 P55789-1
GFERENST00000561710.1 linkc.3C>A p.Asn1Lys missense_variant Exon 1 of 2 2 ENSP00000456189.1 H3BRD2
GFERENST00000569451.1 linkc.42C>A p.Asn14Lys missense_variant Exon 1 of 2 5 ENSP00000456432.1 H3BRW3

Frequencies

GnomAD3 genomes
AF:
0.00000658
AC:
1
AN:
152040
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
7.54e-7
AC:
1
AN:
1326410
Hom.:
0
Cov.:
32
AF XY:
0.00000153
AC XY:
1
AN XY:
653758
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000332
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000658
AC:
1
AN:
152040
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
74258
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.14
BayesDel_addAF
Benign
-0.30
T
BayesDel_noAF
Benign
-0.66
CADD
Benign
0.11
DANN
Benign
0.63
DEOGEN2
Benign
0.10
.;T;T
Eigen
Benign
-1.6
Eigen_PC
Benign
-1.7
FATHMM_MKL
Benign
0.021
N
LIST_S2
Benign
0.60
T;T;D
M_CAP
Benign
0.041
D
MetaRNN
Benign
0.058
T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.0
.;L;.
PrimateAI
Pathogenic
0.82
D
PROVEAN
Benign
-0.81
N;N;N
REVEL
Benign
0.027
Sift
Benign
0.089
T;T;D
Sift4G
Benign
0.19
T;T;D
Polyphen
0.0070
.;B;.
Vest4
0.14
MutPred
0.28
Gain of MoRF binding (P = 0.0312);Gain of MoRF binding (P = 0.0312);.;
MVP
0.51
MPC
0.39
ClinPred
0.11
T
GERP RS
-1.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0
Varity_R
0.043
gMVP
0.21

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: rs1054493594; hg19: chr16-2034261; API