rs261949

chr6-30302303-G-A

Variant summary

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

The NR_024053.2(HCG18):n.804-6066C>T 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 0.287 in 152,100 control chromosomes in the GnomAD database, including 6,755 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 0.29 (6755 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: HCG18 NR_024053.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HCG18	NR_024053.2	n.804-6066C>T		intron_variant, non_coding_transcript_variant
HCG17	NR_052012.1	n.126+23706C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCG17	ENST00000453558.1	n.126+23706C>T		intron_variant, non_coding_transcript_variant		5
HCG18	ENST00000670397.1	n.143-6066C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43581 AN: 151982 Hom.: 6747 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.311

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.287 AC: 43627 AN: 152100 Hom.: 6755 Cov.: 32 AF XY: 0.293 AC XY: 21819 AN XY: 74350

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.313

Alfa AF: 0.255 Hom.: 9314

Bravo AF: 0.295

Asia WGS AF: 0.525 AC: 1826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	5.3
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs261949; hg19: chr6-30270080;