6-30544386-T-C

Variant names:

• chr6-30544386-T-C
• rs1058318
• NM_005275.5:c.*1686A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005275.5(GNL1):​c.*1686A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.729 in 152,126 control chromosomes in the GnomAD database, including 40,795 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 0.73 (40782 hom., cov: 31)
  • Exomes 𝑓: 0.82 (13 hom.)
• Consequence: GNL1 NM_005275.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 24 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GNL1	NM_005275.5	c.*1686A>G		3_prime_UTR_variant	Exon 12 of 12	ENST00000376621.8	NP_005266.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GNL1	ENST00000376621.8	c.*1686A>G		3_prime_UTR_variant	Exon 12 of 12	1	NM_005275.5	ENSP00000365806.3

Frequencies

GnomAD3 genomes AF: 0.728 AC: 110709 AN: 151972 Hom.: 40731 Cov.: 31

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.726

GnomAD4 exome AF: 0.816 AC: 31 AN: 38 Hom.: 13 Cov.: 0 AF XY: 0.864 AC XY: 19 AN XY: 22

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 0.700 AC: 7 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.833 AC: 20 AN: 24

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.729 AC: 110815 AN: 152088 Hom.: 40782 Cov.: 31 AF XY: 0.726 AC XY: 53957 AN XY: 74346

African (AFR) AF: 0.837 AC: 34749 AN: 41500

American (AMR) AF: 0.652 AC: 9973 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.832 AC: 2887 AN: 3472

East Asian (EAS) AF: 0.698 AC: 3607 AN: 5168

South Asian (SAS) AF: 0.825 AC: 3980 AN: 4822

European-Finnish (FIN) AF: 0.680 AC: 7177 AN: 10550

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 45996 AN: 67976

Other (OTH) AF: 0.729 AC: 1538 AN: 2110

Alfa AF: 0.700 Hom.: 133434

Bravo AF: 0.731

Asia WGS AF: 0.783 AC: 2725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.5
DANN	Benign	0.81
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1058318; hg19: chr6-30512163;