ENST00000414046.3:n.4832C>T

Variant names:

• chr6-31468092-C-T
• rs4713466
• ENST00000414046.3:n.4832C>T

Variant summary

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

The ENST00000414046.3(HCP5):​n.4832C>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 0.139 in 151,866 control chromosomes in the GnomAD database, including 1,778 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 0.14 (1778 hom., cov: 32)
• Consequence: HCP5 ENST00000414046.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204
• Publications: 28 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.209 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
HCP5	ENST00000414046.3	n.4832C>T		non_coding_transcript_exon_variant	Exon 2 of 2	4
HCP5	ENST00000467369.2	n.217+4584C>T		intron_variant	Intron 2 of 2	4
HCP5	ENST00000666495.2	n.95+4813C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21113 AN: 151748 Hom.: 1775 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0764

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.139 AC: 21119 AN: 151866 Hom.: 1778 Cov.: 32 AF XY: 0.134 AC XY: 9958 AN XY: 74260

African (AFR) AF: 0.168 AC: 6959 AN: 41312

American (AMR) AF: 0.156 AC: 2371 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 467 AN: 3462

East Asian (EAS) AF: 0.220 AC: 1135 AN: 5158

South Asian (SAS) AF: 0.107 AC: 517 AN: 4814

European-Finnish (FIN) AF: 0.0764 AC: 809 AN: 10590

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8423 AN: 68000

Other (OTH) AF: 0.144 AC: 305 AN: 2112

Alfa AF: 0.126 Hom.: 3269

Bravo AF: 0.147

Asia WGS AF: 0.117 AC: 406 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.57
DANN	Benign	0.39
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs4713466; hg19: chr6-31435869;