chr6-31197789-T-C

Position:

• chr6-31197789-T-C

Variant summary

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

The NR_026791.1(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 NR_026791.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HCG27	NR_026791.1	n.30T>C		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HCG27	ENST00000383331.4	n.30T>C		non_coding_transcript_exon_variant	1/2	1
	ENST00000606367.1	n.249A>G		non_coding_transcript_exon_variant	1/1
HCG27	ENST00000638546.1			upstream_gene_variant		1

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

GnomAD3 exomes AF: 0.863 AC: 112581 AN: 130424 Hom.: 48809 AF XY: 0.864 AC XY: 61489 AN XY: 71198

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 SAS exome AF: 0.854

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

Gnomad4 AFR exome AF: 0.936

Gnomad4 AMR exome AF: 0.850

Gnomad4 ASJ exome AF: 0.971

Gnomad4 EAS exome AF: 0.841

Gnomad4 SAS exome AF: 0.858

Gnomad4 FIN exome AF: 0.851

Gnomad4 NFE exome AF: 0.854

Gnomad4 OTH exome AF: 0.873

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

Gnomad4 AFR AF: 0.941

Gnomad4 AMR AF: 0.894

Gnomad4 ASJ AF: 0.972

Gnomad4 EAS AF: 0.842

Gnomad4 SAS AF: 0.874

Gnomad4 FIN AF: 0.852

Gnomad4 NFE AF: 0.853

Gnomad4 OTH AF: 0.913

Alfa AF: 0.868 Hom.: 101231

Bravo AF: 0.891

Asia WGS AF: 0.877 AC: 3051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs3094609; hg19: chr6-31165566;