6-31197789-T-C

Variant names:

• chr6-31197789-T-C
• rs3094609
• ENST00000383331.4:n.30T>C

Variant summary

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

The ENST00000383331.4(HCG27):​n.30T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.87 in 458,366 control chromosomes in the GnomAD database, including 173,920 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 0.89 (59711 hom., cov: 29)
  • Exomes 𝑓: 0.86 (114209 hom.)
• Consequence: HCG27 ENST00000383331.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 47 publications found

Genes affected

HCG27 (HGNC:27366): (HLA complex group 27)

ENSG00000272501 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000383331.4. 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
	HCG27	NR_026791.1		n.30T>C		non_coding_transcript_exon	Exon 1 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG27	ENST00000383331.4	TSL:1	n.30T>C		non_coding_transcript_exon	Exon 1 of 2
	HCG27	ENST00000638546.2	TSL:1	n.75T>C		non_coding_transcript_exon	Exon 1 of 2
	HCG27	ENST00000424675.3	TSL:3	n.29T>C		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.885 AC: 134455 AN: 151862 Hom.: 59658 Cov.: 29

Gnomad AFR AF: 0.941

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.972

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.915

GnomAD2 exomes AF: 0.863 AC: 112581 AN: 130424 AF XY: 0.864

Gnomad AFR exome AF: 0.942

Gnomad AMR exome AF: 0.848

Gnomad ASJ exome AF: 0.971

Gnomad EAS exome AF: 0.824

Gnomad FIN exome AF: 0.841

Gnomad NFE exome AF: 0.856

Gnomad OTH exome AF: 0.895

GnomAD4 exome AF: 0.862 AC: 264079 AN: 306386 Hom.: 114209 Cov.: 0 AF XY: 0.863 AC XY: 150338 AN XY: 174246

African (AFR) AF: 0.936 AC: 8102 AN: 8652

American (AMR) AF: 0.850 AC: 23188 AN: 27268

Ashkenazi Jewish (ASJ) AF: 0.971 AC: 10487 AN: 10804

East Asian (EAS) AF: 0.841 AC: 7764 AN: 9234

South Asian (SAS) AF: 0.858 AC: 51241 AN: 59752

European-Finnish (FIN) AF: 0.851 AC: 10513 AN: 12358

Middle Eastern (MID) AF: 0.910 AC: 2531 AN: 2780

European-Non Finnish (NFE) AF: 0.854 AC: 137798 AN: 161264

Other (OTH) AF: 0.873 AC: 12455 AN: 14274

GnomAD4 genome AF: 0.885 AC: 134563 AN: 151980 Hom.: 59711 Cov.: 29 AF XY: 0.886 AC XY: 65806 AN XY: 74272

African (AFR) AF: 0.941 AC: 39042 AN: 41468

American (AMR) AF: 0.894 AC: 13634 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.972 AC: 3375 AN: 3472

East Asian (EAS) AF: 0.842 AC: 4331 AN: 5146

South Asian (SAS) AF: 0.874 AC: 4215 AN: 4824

European-Finnish (FIN) AF: 0.852 AC: 8980 AN: 10540

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.853 AC: 58005 AN: 67964

Other (OTH) AF: 0.913 AC: 1922 AN: 2104

Alfa AF: 0.870 Hom.: 231310

Bravo AF: 0.891

Asia WGS AF: 0.877 AC: 3051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.1
DANN	Benign	0.43
PhyloP100		-1.5

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3094609; hg19: chr6-31165566;