ENST00000606367.1:n.288C>T

Variant names:

• chr6-31197750-G-A
• rs28362343
• ENST00000606367.1:n.288C>T

Variant summary

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

The ENST00000606367.1(ENSG00000272501):​n.288C>T 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 0.127 in 454,262 control chromosomes in the GnomAD database, including 4,128 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 0.12 (1236 hom., cov: 32)
  • Exomes 𝑓: 0.13 (2892 hom.)
• Consequence: ENSG00000272501 ENST00000606367.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182

Genes affected

ENSG00000272501 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCG27	NR_026791.1	n.-10G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000272501	ENST00000606367.1	n.288C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
HCG27	ENST00000383331.4	n.-10G>A		upstream_gene_variant		1
HCG27	ENST00000638546.1	n.-87G>A		upstream_gene_variant		1

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18574 AN: 152020 Hom.: 1234 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.173

GnomAD3 exomes AF: 0.140 AC: 18145 AN: 129684 Hom.: 1403 AF XY: 0.139 AC XY: 9842 AN XY: 70840

Gnomad AFR exome AF: 0.106

Gnomad AMR exome AF: 0.190

Gnomad ASJ exome AF: 0.175

Gnomad EAS exome AF: 0.140

Gnomad SAS exome AF: 0.144

Gnomad FIN exome AF: 0.164

Gnomad NFE exome AF: 0.110

Gnomad OTH exome AF: 0.139

GnomAD4 exome AF: 0.130 AC: 39224 AN: 302124 Hom.: 2892 Cov.: 0 AF XY: 0.131 AC XY: 22545 AN XY: 171912

Gnomad4 AFR exome AF: 0.105

Gnomad4 AMR exome AF: 0.191

Gnomad4 ASJ exome AF: 0.173

Gnomad4 EAS exome AF: 0.131

Gnomad4 SAS exome AF: 0.147

Gnomad4 FIN exome AF: 0.159

Gnomad4 NFE exome AF: 0.108

Gnomad4 OTH exome AF: 0.123

GnomAD4 genome AF: 0.122 AC: 18597 AN: 152138 Hom.: 1236 Cov.: 32 AF XY: 0.126 AC XY: 9392 AN XY: 74388

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.173

Alfa AF: 0.122 Hom.: 799

Bravo AF: 0.122

Asia WGS AF: 0.134 AC: 465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.2
DANN	Uncertain	0.98

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28362343; hg19: chr6-31165527; COSMIC: COSV67271546;