Genetic Variant HCP5:n.218-1234T>C (chr6-31475793-T-C) – 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.218-1234T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.885 in 151,688 control chromosomes in the GnomAD database, including 59,615 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 0.89 ( 59615 hom., cov: 29)

Consequence

HCP5
ENST00000467369.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.76

Publications

6 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=-1.06).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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.218-1234T>C	intron_variant	Intron 2 of 2	4
HCP5	ENST00000666495.2 link	n.96-1234T>C	intron_variant	Intron 1 of 1
HCP5	ENST00000674016.2 link	n.889-1234T>C	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.885

AC:

134153

AN:

151570

Hom.:

59555

Cov.:

show subpopulations

Gnomad AFR

AF:

0.897

Gnomad AMI

AF:

0.974

Gnomad AMR

AF:

0.909

Gnomad ASJ

AF:

0.956

Gnomad EAS

AF:

0.983

Gnomad SAS

AF:

0.968

Gnomad FIN

AF:

0.875

Gnomad MID

AF:

0.949

Gnomad NFE

AF:

0.855

Gnomad OTH

AF:

0.911

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

GnomAD4 genome

AF:

0.885

AC:

134271

AN:

151688

Hom.:

59615

Cov.:

AF XY:

0.888

AC XY:

65862

AN XY:

74152

show subpopulations

African (AFR)

AF:

0.897

AC:

36946

AN:

41186

American (AMR)

AF:

0.910

AC:

13844

AN:

15218

Ashkenazi Jewish (ASJ)

AF:

0.956

AC:

3314

AN:

3468

East Asian (EAS)

AF:

0.983

AC:

5059

AN:

5144

South Asian (SAS)

AF:

0.968

AC:

4650

AN:

4806

European-Finnish (FIN)

AF:

0.875

AC:

9246

AN:

10568

Middle Eastern (MID)

AF:

0.942

AC:

277

AN:

294

European-Non Finnish (NFE)

AF:

0.855

AC:

58125

AN:

67986

Other (OTH)

AF:

0.913

AC:

1922

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

756

1512

2267

3023

3779

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

898

1796

2694

3592

4490

<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:

0.869

Hom.:

16205

Bravo

AF:

0.889

Asia WGS

AF:

0.964

AC:

3351

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.79

(source)

DANN

Benign

0.18

PhyloP100

-2.8

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