6-30553360-G-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_005275.5(GNL1):​c.798C>G​(p.Asp266Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 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: not found (cov: 31)

Consequence

GNL1
NM_005275.5 missense

Scores

2
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.108
Variant links:
Genes affected
GNL1 (HGNC:4413): (G protein nucleolar 1 (putative)) The GNL1 gene, identified in the human major histocompatibility complex class I region, shows a high degree of similarity with its mouse counterpart. The GNL1 gene is located less than 2 kb centromeric to HLA-E, in the same transcriptional orientation. GNL1 is telomeric to HLA-B and HLA-C. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.060096443).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GNL1NM_005275.5 linkc.798C>G p.Asp266Glu missense_variant Exon 6 of 12 ENST00000376621.8 NP_005266.2 P36915-1A0A024RCR2B4DYK6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GNL1ENST00000376621.8 linkc.798C>G p.Asp266Glu missense_variant Exon 6 of 12 1 NM_005275.5 ENSP00000365806.3 P36915-1
GNL1ENST00000433809.1 linkc.792C>G p.Asp264Glu missense_variant, splice_region_variant Exon 5 of 5 2 ENSP00000404728.1 A2AB27
GNL1ENST00000487166.1 linkn.-240C>G upstream_gene_variant 3

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
37
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.13
BayesDel_addAF
Benign
-0.34
T
BayesDel_noAF
Benign
-0.72
CADD
Benign
12
DANN
Uncertain
1.0
DEOGEN2
Benign
0.010
T;.
Eigen
Benign
-0.73
Eigen_PC
Benign
-0.59
FATHMM_MKL
Benign
0.32
N
M_CAP
Benign
0.0041
T
MetaRNN
Benign
0.040
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.4
L;.
PrimateAI
Uncertain
0.53
T
PROVEAN
Benign
-0.040
N;N
REVEL
Benign
0.059
Sift
Benign
0.82
T;T
Sift4G
Benign
1.0
T;T
Polyphen
0.0060
B;.
Vest4
0.039
MutPred
0.28
Gain of sheet (P = 0.0061);.;
MVP
0.16
MPC
0.61
ClinPred
0.18
T
GERP RS
2.6
Varity_R
0.039
gMVP
0.48

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-30521137; API