ENST00000755328.1:n.161+2703G>C

Variant names:

• chr6-31206813-G-C
• rs2394885
• ENST00000755328.1:n.161+2703G>C

Variant summary

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

The ENST00000755328.1(HCG27):​n.161+2703G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,088 control chromosomes in the GnomAD database, including 1,404 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 0.13 (1404 hom., cov: 31)
• Consequence: HCG27 ENST00000755328.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197
• Publications: 9 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCG27	ENST00000755328.1	n.161+2703G>C		intron_variant	Intron 2 of 2
HCG27	ENST00000755329.1	n.160-1601G>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20346 AN: 151970 Hom.: 1404 Cov.: 31

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0882

Gnomad EAS AF: 0.0412

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.129

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.134 AC: 20353 AN: 152088 Hom.: 1404 Cov.: 31 AF XY: 0.132 AC XY: 9793 AN XY: 74362

African (AFR) AF: 0.133 AC: 5503 AN: 41486

American (AMR) AF: 0.109 AC: 1672 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0882 AC: 306 AN: 3470

East Asian (EAS) AF: 0.0417 AC: 216 AN: 5182

South Asian (SAS) AF: 0.134 AC: 646 AN: 4814

European-Finnish (FIN) AF: 0.136 AC: 1435 AN: 10578

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.149 AC: 10126 AN: 67966

Other (OTH) AF: 0.128 AC: 271 AN: 2110

Alfa AF: 0.143 Hom.: 191

Bravo AF: 0.132

Asia WGS AF: 0.128 AC: 445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.3
DANN	Benign	0.40
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs2394885; hg19: chr6-31174590;