Genetic Variant HCP5:n.218-4252T>G (chr6-31472775-T-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.218-4252T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 151,722 control chromosomes in the GnomAD database, including 9,199 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 0.33 ( 9199 hom., cov: 32)

Consequence

HCP5
ENST00000467369.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.921

Publications

13 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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 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.218-4252T>G	intron_variant	Intron 2 of 2	4
HCP5	ENST00000666495.2 link	n.96-4252T>G	intron_variant	Intron 1 of 1
HCP5	ENST00000674016.2 link	n.889-4252T>G	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.331

AC:

50169

AN:

151604

Hom.:

9168

Cov.:

show subpopulations

Gnomad AFR

AF:

0.449

Gnomad AMI

AF:

0.337

Gnomad AMR

AF:

0.281

Gnomad ASJ

AF:

0.500

Gnomad EAS

AF:

0.311

Gnomad SAS

AF:

0.307

Gnomad FIN

AF:

0.359

Gnomad MID

AF:

0.516

Gnomad NFE

AF:

0.259

Gnomad OTH

AF:

0.364

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

GnomAD4 genome

AF:

0.331

AC:

50249

AN:

151722

Hom.:

9199

Cov.:

AF XY:

0.332

AC XY:

24621

AN XY:

74142

show subpopulations

African (AFR)

AF:

0.450

AC:

18562

AN:

41248

American (AMR)

AF:

0.281

AC:

4271

AN:

15206

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

1733

AN:

3468

East Asian (EAS)

AF:

0.311

AC:

1607

AN:

5162

South Asian (SAS)

AF:

0.306

AC:

1474

AN:

4812

European-Finnish (FIN)

AF:

0.359

AC:

3792

AN:

10566

Middle Eastern (MID)

AF:

0.517

AC:

152

AN:

294

European-Non Finnish (NFE)

AF:

0.259

AC:

17587

AN:

67946

Other (OTH)

AF:

0.362

AC:

764

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1642

3285

4927

6570

8212

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

496

992

1488

1984

2480

<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:

0.285

Hom.:

11893

Bravo

AF:

0.330

Asia WGS

AF:

0.382

AC:

1329

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

2.0

(source)

DANN

Benign

0.39

PhyloP100

-0.92

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