dbSNP rs17206855: HCP5:n.197+254T>C (chr6-31463762-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 ENST00000541196.3(HCP5):n.197+254T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0194 in 434,256 control chromosomes in the GnomAD database, including 276 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 0.024 ( 120 hom., cov: 32)

Exomes 𝑓: 0.017 ( 156 hom. )

Consequence

HCP5
ENST00000541196.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.159

Publications

3 publications found

Variant links:

COSMIC-nc: COSV69993903

Genes affected

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

HCP5 links:

ENSG00000288587 (HGNC:):

ENSG00000288587 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=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCP5	NR_040662.1 link	n.492T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
HCP5	ENST00000541196.3 link	n.197+254T>C	intron_variant	Intron 2 of 3	1
HCP5	ENST00000414046.3 link	n.502T>C	non_coding_transcript_exon_variant	Exon 2 of 2	4
HCP5	ENST00000460889.5 link	n.406T>C	non_coding_transcript_exon_variant	Exon 3 of 3	2

Frequencies

GnomAD3 genomes

AF:

0.0241

AC:

3664

AN:

151876

Hom.:

120

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0564

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0246

Gnomad ASJ

AF:

0.0167

Gnomad EAS

AF:

0.00657

Gnomad SAS

AF:

0.0735

Gnomad FIN

AF:

0.00151

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.00644

Gnomad OTH

AF:

0.0254

GnomAD2 exomes

AF:

0.0156

AC:

2614

AN:

167452

AF XY:

0.0162

show subpopulations

Gnomad AFR exome

AF:

0.0601

Gnomad AMR exome

AF:

0.0109

Gnomad ASJ exome

AF:

0.0158

Gnomad EAS exome

AF:

0.0103

Gnomad FIN exome

AF:

0.00191

Gnomad NFE exome

AF:

0.00627

Gnomad OTH exome

AF:

0.0106

GnomAD4 exome

AF:

0.0169

AC:

4780

AN:

282262

Hom.:

156

Cov.:

AF XY:

0.0209

AC XY:

3353

AN XY:

160510

show subpopulations

African (AFR)

AF:

0.0604

AC:

389

AN:

6438

American (AMR)

AF:

0.0108

AC:

207

AN:

19224

Ashkenazi Jewish (ASJ)

AF:

0.0179

AC:

107

AN:

5986

East Asian (EAS)

AF:

0.0117

AC:

114

AN:

9738

South Asian (SAS)

AF:

0.0559

AC:

2818

AN:

50446

European-Finnish (FIN)

AF:

0.00258

AC:

AN:

29458

Middle Eastern (MID)

AF:

0.0139

AC:

AN:

2440

European-Non Finnish (NFE)

AF:

0.00581

AC:

849

AN:

146142

Other (OTH)

AF:

0.0150

AC:

186

AN:

12390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

211

422

634

845

1056

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

102

136

170

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0241

AC:

3665

AN:

151994

Hom.:

120

Cov.:

AF XY:

0.0244

AC XY:

1816

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.0563

AC:

2329

AN:

41364

American (AMR)

AF:

0.0246

AC:

375

AN:

15238

Ashkenazi Jewish (ASJ)

AF:

0.0167

AC:

AN:

3470

East Asian (EAS)

AF:

0.00678

AC:

AN:

5162

South Asian (SAS)

AF:

0.0731

AC:

352

AN:

4814

European-Finnish (FIN)

AF:

0.00151

AC:

AN:

10618

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00643

AC:

437

AN:

68010

Other (OTH)

AF:

0.0251

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

174

347

521

694

868

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

152

190

<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:

0.0143

Hom.:

Bravo

AF:

0.0264

Asia WGS

AF:

0.0370

AC:

128

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

6.8

(source)

DANN

Benign

0.092

PhyloP100

0.16

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over