rs16899682

Positions:

• chr6-31475922-G-C

Variant summary

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

The ENST00000666495.2(HCP5):​n.96-1105G>C 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 0.039 in 151,876 control chromosomes in the GnomAD database, including 227 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 0.039 (227 hom., cov: 32)
• Consequence: HCP5 ENST00000666495.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.912

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0773 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HCP5	ENST00000666495.2	n.96-1105G>C		intron_variant, non_coding_transcript_variant
HCP5	ENST00000467369.2	n.218-1105G>C		intron_variant, non_coding_transcript_variant		4
HCP5	ENST00000674016.1	n.98-1105G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0388 AC: 5893 AN: 151758 Hom.: 222 Cov.: 32

Gnomad AFR AF: 0.0790

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.0265

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.00252

Gnomad SAS AF: 0.0102

Gnomad FIN AF: 0.0292

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0237

Gnomad OTH AF: 0.0326

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

GnomAD4 genome AF: 0.0390 AC: 5921 AN: 151876 Hom.: 227 Cov.: 32 AF XY: 0.0389 AC XY: 2884 AN XY: 74232

Gnomad4 AFR AF: 0.0795

Gnomad4 AMR AF: 0.0264

Gnomad4 ASJ AF: 0.0297

Gnomad4 EAS AF: 0.00252

Gnomad4 SAS AF: 0.00997

Gnomad4 FIN AF: 0.0292

Gnomad4 NFE AF: 0.0236

Gnomad4 OTH AF: 0.0323

Alfa AF: 0.0283 Hom.: 14

Bravo AF: 0.0397

Asia WGS AF: 0.0110 AC: 39 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16899682; hg19: chr6-31443699;