rs12660382

chr6-31475546-C-T

Variant summary

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

The ENST00000666495.2(HCP5):n.96-1481C>T variant causes a intron, non coding transcript 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 ENST00000666495.2 intron, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCP5	ENST00000666495.2	n.96-1481C>T		intron_variant, non_coding_transcript_variant
HCP5	ENST00000467369.2	n.218-1481C>T		intron_variant, non_coding_transcript_variant		4
HCP5	ENST00000674016.1	n.98-1481C>T		intron_variant, non_coding_transcript_variant

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;