6-31470817-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000414046.3(HCP5):​n.7557C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.786 in 151,716 control chromosomes in the GnomAD database, including 47,336 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 0.79 ( 47336 hom., cov: 31)

Consequence

HCP5
ENST00000414046.3 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.201
Variant links:
Genes affected
HCP5 (HGNC:21659): (HLA complex P5)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
HCP5ENST00000414046.3 linkn.7557C>T non_coding_transcript_exon_variant Exon 2 of 2 4
HCP5ENST00000467369.2 linkn.218-6210C>T intron_variant Intron 2 of 2 4
HCP5ENST00000666495.2 linkn.96-6210C>T intron_variant Intron 1 of 1
HCP5ENST00000674016.1 linkn.98-6210C>T intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
AF:
0.786
AC:
119139
AN:
151598
Hom.:
47270
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.857
Gnomad AMI
AF:
0.838
Gnomad AMR
AF:
0.826
Gnomad ASJ
AF:
0.817
Gnomad EAS
AF:
0.902
Gnomad SAS
AF:
0.768
Gnomad FIN
AF:
0.741
Gnomad MID
AF:
0.779
Gnomad NFE
AF:
0.731
Gnomad OTH
AF:
0.800
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.786
AC:
119266
AN:
151716
Hom.:
47336
Cov.:
31
AF XY:
0.786
AC XY:
58339
AN XY:
74180
show subpopulations
Gnomad4 AFR
AF:
0.857
Gnomad4 AMR
AF:
0.826
Gnomad4 ASJ
AF:
0.817
Gnomad4 EAS
AF:
0.902
Gnomad4 SAS
AF:
0.769
Gnomad4 FIN
AF:
0.741
Gnomad4 NFE
AF:
0.731
Gnomad4 OTH
AF:
0.802
Alfa
AF:
0.744
Hom.:
11102
Bravo
AF:
0.799
Asia WGS
AF:
0.811
AC:
2821
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
1.7
DANN
Benign
0.099

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.

Other links and lift over

dbSNP: rs2523666; hg19: chr6-31438594; API