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

Variant summary

Our verdict is Benign. Variant got -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

Variant links:

Genes affected

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

HCP5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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	ENST00000674016.1 link	n.98-4135C>G	intron_variant	Intron 1 of 1

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

Gnomad4 AFR

AF:

0.298

Gnomad4 AMR

AF:

0.137

Gnomad4 ASJ

AF:

0.168

Gnomad4 EAS

AF:

0.0371

Gnomad4 SAS

AF:

0.0698

Gnomad4 FIN

AF:

0.222

Gnomad4 NFE

AF:

0.104

Gnomad4 OTH

AF:

0.175

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

DANN

Benign

0.68

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over