ENST00000426882.6:n.798-6066C>T

Variant names:

• chr6-30302303-G-A
• rs261949
• ENST00000426882.6:n.798-6066C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000426882.6(HCG18):​n.798-6066C>T variant causes a intron 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 ENST00000426882.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100
• Publications: 26 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000426882.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG18	NR_024052.2		n.1018-6066C>T		intron	N/A
	HCG18	NR_024053.2		n.804-6066C>T		intron	N/A
	HCG17	NR_052012.1		n.126+23706C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG18	ENST00000426882.6	TSL:1	n.798-6066C>T		intron	N/A
	HCG18	ENST00000602319.2	TSL:6	n.2243C>T		non_coding_transcript_exon	Exon 3 of 3
	HCG18	ENST00000412685.10	TSL:2	n.534-6066C>T		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.291 AC: 12058 AN: 41488

American (AMR) AF: 0.391 AC: 5971 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1408 AN: 3472

East Asian (EAS) AF: 0.491 AC: 2539 AN: 5172

South Asian (SAS) AF: 0.499 AC: 2405 AN: 4816

European-Finnish (FIN) AF: 0.274 AC: 2892 AN: 10562

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15284 AN: 67990

Other (OTH) AF: 0.313 AC: 659 AN: 2104

Alfa AF: 0.260 Hom.: 16655

Bravo AF: 0.295

Asia WGS AF: 0.525 AC: 1826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.3
DANN	Benign	0.76
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs261949; hg19: chr6-30270080;