6-30317535-G-C

Variant names:

• chr6-30317535-G-C
• rs3094628
• ENST00000426882.6:n.797+8819C>G

Variant summary

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

The ENST00000426882.6(HCG18):​n.797+8819C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.06 in 152,212 control chromosomes in the GnomAD database, including 460 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 0.060 (460 hom., cov: 32)
• Consequence: HCG18 ENST00000426882.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470
• Publications: 16 publications found

Genes affected

HCG18 (HGNC:31337): (HLA complex group 18)

HCG17 (HGNC:31339): (HLA complex group 17)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCG18	NR_024052.2	n.804-3053C>G		intron_variant	Intron 1 of 4
HCG18	NR_024053.2	n.803+8819C>G		intron_variant	Intron 1 of 3
HCG17	NR_052012.1	n.126+8474C>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCG18	ENST00000426882.6	n.797+8819C>G		intron_variant	Intron 1 of 2	1
HCG18	ENST00000412685.10	n.533+8819C>G		intron_variant	Intron 1 of 2	2
HCG18	ENST00000413358.6	n.39-3053C>G		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.0601 AC: 9139 AN: 152094 Hom.: 460 Cov.: 32

Gnomad AFR AF: 0.0149

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0238

Gnomad ASJ AF: 0.0302

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.000208

Gnomad FIN AF: 0.0695

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0379

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0600 AC: 9136 AN: 152212 Hom.: 460 Cov.: 32 AF XY: 0.0548 AC XY: 4080 AN XY: 74414

African (AFR) AF: 0.0149 AC: 617 AN: 41544

American (AMR) AF: 0.0237 AC: 363 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0302 AC: 105 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5188

South Asian (SAS) AF: 0.000208 AC: 1 AN: 4812

European-Finnish (FIN) AF: 0.0695 AC: 736 AN: 10594

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7078 AN: 67998

Other (OTH) AF: 0.0375 AC: 79 AN: 2106

Alfa AF: 0.0459 Hom.: 50

Bravo AF: 0.0552

Asia WGS AF: 0.00346 AC: 13 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.5
DANN	Benign	0.50
PhyloP100		0.047
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3094628; hg19: chr6-30285312;