ENST00000467369.2:n.218-4135C>G

Variant names:

• chr6-31472892-C-G
• rs3828890
• ENST00000467369.2:n.218-4135C>G

Variant summary

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

The ENST00000467369.2(HCP5):​n.218-4135C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 151,948 control chromosomes in the GnomAD database, including 2,982 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 0.17 (2982 hom., cov: 32)
• Consequence: HCP5 ENST00000467369.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.634
• Publications: 16 publications found

Genes affected

HCP5 (HGNC:21659): (HLA complex P5)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000467369.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCP5	ENST00000467369.2	TSL:4	n.218-4135C>G		intron	N/A
	HCP5	ENST00000666495.2		n.96-4135C>G		intron	N/A
	HCP5	ENST00000674016.2		n.889-4135C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25518 AN: 151830 Hom.: 2968 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.0370

Gnomad SAS AF: 0.0700

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.168 AC: 25570 AN: 151948 Hom.: 2982 Cov.: 32 AF XY: 0.170 AC XY: 12596 AN XY: 74276

African (AFR) AF: 0.298 AC: 12309 AN: 41340

American (AMR) AF: 0.137 AC: 2086 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 581 AN: 3466

East Asian (EAS) AF: 0.0371 AC: 192 AN: 5172

South Asian (SAS) AF: 0.0698 AC: 337 AN: 4826

European-Finnish (FIN) AF: 0.222 AC: 2349 AN: 10592

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7072 AN: 68012

Other (OTH) AF: 0.175 AC: 369 AN: 2106

Alfa AF: 0.0586 Hom.: 68

Bravo AF: 0.169

Asia WGS AF: 0.0770 AC: 272 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.6
DANN	Benign	0.68
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs3828890; hg19: chr6-31440669;