6-31197789-T-A

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000383331.4(HCG27):​n.30T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 29)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).

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>A		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>A		non_coding_transcript_exon	Exon 1 of 2
	HCG27	ENST00000638546.2	TSL:1	n.75T>A		non_coding_transcript_exon	Exon 1 of 2
	HCG27	ENST00000424675.3	TSL:3	n.29T>A		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 306438 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 174274

African (AFR) AF: 0.00 AC: 0 AN: 8652

American (AMR) AF: 0.00 AC: 0 AN: 27278

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10804

East Asian (EAS) AF: 0.00 AC: 0 AN: 9236

South Asian (SAS) AF: 0.00 AC: 0 AN: 59754

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12364

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2780

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 161292

Other (OTH) AF: 0.00 AC: 0 AN: 14278

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.6
DANN	Benign	0.49
PhyloP100		-1.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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;