6-30317535-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_024053.2(HCG18):n.803+8819C>G variant causes a intron, non coding transcript 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 NR_024053.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
HCG18	NR_024053.2	n.803+8819C>G		intron_variant, non_coding_transcript_variant
HCG17	NR_052012.1	n.126+8474C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCG17	ENST00000453558.1	n.126+8474C>G		intron_variant, non_coding_transcript_variant		5
HCG18	ENST00000670397.1	n.142+9686C>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0149

Gnomad4 AMR AF: 0.0237

Gnomad4 ASJ AF: 0.0302

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.000208

Gnomad4 FIN AF: 0.0695

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0375

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
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

Publications

LitVar

Other links and lift over

dbSNP: rs3094628; hg19: chr6-30285312;