Genetic Variant HCP5:n.218-4135C>G (chr6-31472892-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000467369.2(HCP5):n.218-4135C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 151,948 control chromosomes in the GnomAD database, including 2,982 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 0.17 ( 2982 hom., cov: 32)

Consequence

HCP5
ENST00000467369.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.634

Publications

16 publications found

Variant links:

Genes affected

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

HCP5 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
HCP5	ENST00000467369.2 link	n.218-4135C>G	intron_variant	Intron 2 of 2	4
HCP5	ENST00000666495.2 link	n.96-4135C>G	intron_variant	Intron 1 of 1
HCP5	ENST00000674016.2 link	n.889-4135C>G	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.168

AC:

25518

AN:

151830

Hom.:

2968

Cov.:

show subpopulations

Gnomad AFR

AF:

0.297

Gnomad AMI

AF:

0.255

Gnomad AMR

AF:

0.137

Gnomad ASJ

AF:

0.168

Gnomad EAS

AF:

0.0370

Gnomad SAS

AF:

0.0700

Gnomad FIN

AF:

0.222

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.104

Gnomad OTH

AF:

0.177

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

GnomAD4 genome

AF:

0.168

AC:

25570

AN:

151948

Hom.:

2982

Cov.:

AF XY:

0.170

AC XY:

12596

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.298

AC:

12309

AN:

41340

American (AMR)

AF:

0.137

AC:

2086

AN:

15228

Ashkenazi Jewish (ASJ)

AF:

0.168

AC:

581

AN:

3466

East Asian (EAS)

AF:

0.0371

AC:

192

AN:

5172

South Asian (SAS)

AF:

0.0698

AC:

337

AN:

4826

European-Finnish (FIN)

AF:

0.222

AC:

2349

AN:

10592

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.104

AC:

7072

AN:

68012

Other (OTH)

AF:

0.175

AC:

369

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1005

2010

3016

4021

5026

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

262

524

786

1048

1310

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0586

Hom.:

Bravo

AF:

0.169

Asia WGS

AF:

0.0770

AC:

272

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.6

(source)

DANN

Benign

0.68

PhyloP100

0.63

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over