rs16899682

Variant names:

• chr6-31475922-G-C
• rs16899682
• ENST00000467369.2:n.218-1105G>C

Variant summary

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

The ENST00000467369.2(HCP5):​n.218-1105G>C variant causes a intron 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 ENST00000467369.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.912
• Publications: 8 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0773 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCP5	ENST00000467369.2	TSL:4	n.218-1105G>C		intron	N/A
	HCP5	ENST00000666495.2		n.96-1105G>C		intron	N/A
	HCP5	ENST00000674016.2		n.889-1105G>C		intron	N/A

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

African (AFR) AF: 0.0795 AC: 3286 AN: 41316

American (AMR) AF: 0.0264 AC: 402 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.0297 AC: 103 AN: 3472

East Asian (EAS) AF: 0.00252 AC: 13 AN: 5154

South Asian (SAS) AF: 0.00997 AC: 48 AN: 4816

European-Finnish (FIN) AF: 0.0292 AC: 309 AN: 10584

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0236 AC: 1608 AN: 68006

Other (OTH) AF: 0.0323 AC: 68 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.43
PhyloP100		-0.91
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs16899682; hg19: chr6-31443699;