rs12660382

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 32 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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCP5	ENST00000467369.2	TSL:4	n.218-1481C>T		intron	N/A
	HCP5	ENST00000666495.2		n.96-1481C>T		intron	N/A
	HCP5	ENST00000674016.2		n.889-1481C>T		intron	N/A

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

African (AFR) AF: 0.168 AC: 6917 AN: 41198

American (AMR) AF: 0.156 AC: 2381 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1298 AN: 3468

East Asian (EAS) AF: 0.285 AC: 1468 AN: 5144

South Asian (SAS) AF: 0.284 AC: 1364 AN: 4802

European-Finnish (FIN) AF: 0.146 AC: 1543 AN: 10566

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.189 AC: 12874 AN: 67990

Other (OTH) AF: 0.215 AC: 454 AN: 2112

Alfa AF: 0.194 Hom.: 11860

Bravo AF: 0.187

Asia WGS AF: 0.334 AC: 1159 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.2
DANN	Benign	0.85
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs12660382; hg19: chr6-31443323;