Genetic Variant ENST00000467369.2:n.218-1481C>T (chr6-31475546-C-T) – 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.218-1481C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 151,706 control chromosomes in the GnomAD database, including 3,066 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 ( 3066 hom., cov: 32)

Consequence

HCP5
ENST00000467369.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.256

Publications

32 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=-0.77).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 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.218-1481C>T	intron_variant	Intron 2 of 2	4
HCP5	ENST00000666495.2 link	n.96-1481C>T	intron_variant	Intron 1 of 1
HCP5	ENST00000674016.2 link	n.889-1481C>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.189

AC:

28602

AN:

151586

Hom.:

3059

Cov.:

show subpopulations

Gnomad AFR

AF:

0.168

Gnomad AMI

AF:

0.232

Gnomad AMR

AF:

0.156

Gnomad ASJ

AF:

0.374

Gnomad EAS

AF:

0.285

Gnomad SAS

AF:

0.285

Gnomad FIN

AF:

0.146

Gnomad MID

AF:

0.392

Gnomad NFE

AF:

0.189

Gnomad OTH

AF:

0.215

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

GnomAD4 genome

AF:

0.189

AC:

28630

AN:

151706

Hom.:

3066

Cov.:

AF XY:

0.188

AC XY:

13930

AN XY:

74136

show subpopulations

African (AFR)

AF:

0.168

AC:

6917

AN:

41198

American (AMR)

AF:

0.156

AC:

2381

AN:

15222

Ashkenazi Jewish (ASJ)

AF:

0.374

AC:

1298

AN:

3468

East Asian (EAS)

AF:

0.285

AC:

1468

AN:

5144

South Asian (SAS)

AF:

0.284

AC:

1364

AN:

4802

European-Finnish (FIN)

AF:

0.146

AC:

1543

AN:

10566

Middle Eastern (MID)

AF:

0.408

AC:

119

AN:

292

European-Non Finnish (NFE)

AF:

0.189

AC:

12874

AN:

67990

Other (OTH)

AF:

0.215

AC:

454

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1144

2289

3433

4578

5722

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

316

632

948

1264

1580

<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:

0.194

Hom.:

11860

Bravo

AF:

0.187

Asia WGS

AF:

0.334

AC:

1159

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

7.2

(source)

DANN

Benign

0.85

PhyloP100

-0.26

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