chr6-30314555-T-C

Position:

• chr6-30314555-T-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+11799A>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 0.917 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 NR_024053.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.720

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=-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/exons	MANE	UniProt
HCG18	NR_024053.2	n.803+11799A>G		intron_variant, non_coding_transcript_variant
HCG17	NR_052012.1	n.126+11454A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCG17	ENST00000453558.1	n.126+11454A>G		intron_variant, non_coding_transcript_variant		5
HCG18	ENST00000670397.1	n.142+12666A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.965

Gnomad4 AMR AF: 0.932

Gnomad4 ASJ AF: 0.951

Gnomad4 EAS AF: 0.974

Gnomad4 SAS AF: 0.948

Gnomad4 FIN AF: 0.895

Gnomad4 NFE AF: 0.878

Gnomad4 OTH AF: 0.920

Alfa AF: 0.893 Hom.: 103526

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
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

Publications

LitVar

Other links and lift over

dbSNP: rs3094065; hg19: chr6-30282332;