rs12660382

Variant names:

• chr6-31475546-C-T
• rs12660382
• ENST00000467369.2:n.218-1481C>T

Variant summary

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

The ENST00000467369.2(HCP5):​n.218-1481C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 151,706 control chromosomes in the GnomAD database, including 3,066 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 0.19 (3066 hom., cov: 32)
• Consequence: HCP5 ENST00000467369.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 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	ENST00000467369.2	n.218-1481C>T		intron_variant	Intron 2 of 2	4
HCP5	ENST00000666495.2	n.96-1481C>T		intron_variant	Intron 1 of 1
HCP5	ENST00000674016.1	n.98-1481C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28602 AN: 151586 Hom.: 3059 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.189 AC: 28630 AN: 151706 Hom.: 3066 Cov.: 32 AF XY: 0.188 AC XY: 13930 AN XY: 74136

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.215

Alfa AF: 0.203 Hom.: 5029

Bravo AF: 0.187

Asia WGS AF: 0.334 AC: 1159 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.2
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12660382; hg19: chr6-31443323;