rs3094065

Variant names:

• chr6-30314555-T-C
• rs3094065
• ENST00000426882.6:n.797+11799A>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+11799A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.917 in 152,270 control chromosomes in the GnomAD database, including 64,114 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 0.92 (64114 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: HCG18 ENST00000426882.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.720
• Publications: 24 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCG18	NR_024052.2	n.804-73A>G		intron_variant	Intron 1 of 4
HCG18	NR_024053.2	n.803+11799A>G		intron_variant	Intron 1 of 3
HCG17	NR_052012.1	n.126+11454A>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+11799A>G		intron_variant	Intron 1 of 2	1
HCG18	ENST00000412685.10	n.533+11799A>G		intron_variant	Intron 1 of 2	2
HCG18	ENST00000413358.6	n.39-73A>G		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.916 AC: 139441 AN: 152152 Hom.: 64052 Cov.: 32

Gnomad AFR AF: 0.965

Gnomad AMI AF: 0.943

Gnomad AMR AF: 0.932

Gnomad ASJ AF: 0.951

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.895

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.917 AC: 139562 AN: 152270 Hom.: 64114 Cov.: 32 AF XY: 0.918 AC XY: 68312 AN XY: 74438

African (AFR) AF: 0.965 AC: 40109 AN: 41560

American (AMR) AF: 0.932 AC: 14255 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.951 AC: 3301 AN: 3472

East Asian (EAS) AF: 0.974 AC: 5053 AN: 5188

South Asian (SAS) AF: 0.948 AC: 4572 AN: 4822

European-Finnish (FIN) AF: 0.895 AC: 9480 AN: 10598

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.878 AC: 59709 AN: 68020

Other (OTH) AF: 0.920 AC: 1945 AN: 2114

Alfa AF: 0.895 Hom.: 240843

Bravo AF: 0.924

Asia WGS AF: 0.960 AC: 3338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.1
DANN	Benign	0.76
PhyloP100		-0.72
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Other links and lift over

dbSNP: rs3094065; hg19: chr6-30282332;