Genetic Variant HCP5:n.218-1234T>C (chr6-31475793-T-C) – 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.218-1234T>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

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=-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	ENST00000674016.1 link	n.98-1234T>C	intron_variant	Intron 1 of 1

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

Gnomad4 AFR

AF:

0.897

Gnomad4 AMR

AF:

0.910

Gnomad4 ASJ

AF:

0.956

Gnomad4 EAS

AF:

0.983

Gnomad4 SAS

AF:

0.968

Gnomad4 FIN

AF:

0.875

Gnomad4 NFE

AF:

0.855

Gnomad4 OTH

AF:

0.913

Alfa

AF:

0.868

Hom.:

15887

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

DANN

Benign

0.18

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