Genetic Variant HCP5:n.96-11643G>A (chr6-31479019-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000718213.1(HCP5):n.96-11643G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 151,792 control chromosomes in the GnomAD database, including 3,184 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 ( 3184 hom., cov: 32)

Consequence

HCP5
ENST00000718213.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.133

Publications

64 publications found

Variant links:

Genes affected

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

HCP5 links:

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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=-0.9).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
HCP5	ENST00000718213.1 link	n.96-11643G>A	intron_variant	Intron 1 of 2
HCP5	ENST00000718214.1 link	n.96-11643G>A	intron_variant	Intron 1 of 2
HCP5	ENST00000666495.2 link	n.*83G>A	downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.194

AC:

29427

AN:

151670

Hom.:

3179

Cov.:

show subpopulations

Gnomad AFR

AF:

0.138

Gnomad AMI

AF:

0.318

Gnomad AMR

AF:

0.260

Gnomad ASJ

AF:

0.185

Gnomad EAS

AF:

0.169

Gnomad SAS

AF:

0.207

Gnomad FIN

AF:

0.164

Gnomad MID

AF:

0.156

Gnomad NFE

AF:

0.218

Gnomad OTH

AF:

0.198

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

GnomAD4 genome

AF:

0.194

AC:

29452

AN:

151792

Hom.:

3184

Cov.:

AF XY:

0.194

AC XY:

14419

AN XY:

74212

show subpopulations

African (AFR)

AF:

0.138

AC:

5700

AN:

41320

American (AMR)

AF:

0.261

AC:

3962

AN:

15206

Ashkenazi Jewish (ASJ)

AF:

0.185

AC:

644

AN:

3472

East Asian (EAS)

AF:

0.170

AC:

873

AN:

5148

South Asian (SAS)

AF:

0.207

AC:

995

AN:

4810

European-Finnish (FIN)

AF:

0.164

AC:

1735

AN:

10578

Middle Eastern (MID)

AF:

0.158

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.218

AC:

14787

AN:

67952

Other (OTH)

AF:

0.200

AC:

422

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1186

2371

3557

4742

5928

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

320

640

960

1280

1600

<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:

0.209

Hom.:

14100

Bravo

AF:

0.201

Asia WGS

AF:

0.172

AC:

600

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.0

(source)

DANN

Benign

0.28

PhyloP100

-0.13

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