rs3094628

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr6-30317535-G-A
• chr6-30317535-G-C
• chr6-30317535-G-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000426882.6(HCG18):​n.797+8819C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000328 in 152,222 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00033 (0 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCG18	NR_024052.2	n.804-3053C>T		intron_variant	Intron 1 of 4
HCG18	NR_024053.2	n.803+8819C>T		intron_variant	Intron 1 of 3
HCG17	NR_052012.1	n.126+8474C>T		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>T		intron_variant	Intron 1 of 2	1
HCG18	ENST00000412685.10	n.533+8819C>T		intron_variant	Intron 1 of 2	2
HCG18	ENST00000413358.6	n.39-3053C>T		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.000329 AC: 50 AN: 152104 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00118

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: 0.0000147

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.000328 AC: 50 AN: 152222 Hom.: 0 Cov.: 32 AF XY: 0.000296 AC XY: 22 AN XY: 74418

African (AFR) AF: 0.00118 AC: 49 AN: 41546

American (AMR) AF: 0.00 AC: 0 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.00 AC: 0 AN: 4812

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10594

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000147 AC: 1 AN: 68002

Other (OTH) AF: 0.00 AC: 0 AN: 2108

Alfa AF: 0.00 Hom.: 50

Bravo AF: 0.000355

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.9
DANN	Benign	0.52
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;