dbSNP rs2255221: HCP5:n.198-139G>T (chr6-31463914-G-T) – 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.198-139G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0729 in 527,838 control chromosomes in the GnomAD database, including 2,374 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 0.098 ( 1018 hom., cov: 32)

Exomes 𝑓: 0.063 ( 1356 hom. )

Consequence

HCP5
ENST00000541196.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.186

Publications

40 publications found

Variant links:

COSMIC-nc: COSV69992164

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=-0.78).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCP5	NR_040662.1 link	n.644G>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
HCP5	ENST00000541196.3 link	n.198-139G>T	intron_variant	Intron 2 of 3	1
HCP5	ENST00000414046.3 link	n.654G>T	non_coding_transcript_exon_variant	Exon 2 of 2	4
HCP5	ENST00000670109.1 link	n.617G>T	non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0982

AC:

14893

AN:

151700

Hom.:

1018

Cov.:

show subpopulations

Gnomad AFR

AF:

0.159

Gnomad AMI

AF:

0.0274

Gnomad AMR

AF:

0.127

Gnomad ASJ

AF:

0.177

Gnomad EAS

AF:

0.0163

Gnomad SAS

AF:

0.0110

Gnomad FIN

AF:

0.0101

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.0775

Gnomad OTH

AF:

0.125

GnomAD2 exomes

AF:

0.0692

AC:

16818

AN:

242966

AF XY:

0.0642

show subpopulations

Gnomad AFR exome

AF:

0.157

Gnomad AMR exome

AF:

0.103

Gnomad ASJ exome

AF:

0.168

Gnomad EAS exome

AF:

0.0126

Gnomad FIN exome

AF:

0.0122

Gnomad NFE exome

AF:

0.0722

Gnomad OTH exome

AF:

0.0927

GnomAD4 exome

AF:

0.0628

AC:

23603

AN:

376020

Hom.:

1356

Cov.:

AF XY:

0.0574

AC XY:

12314

AN XY:

214602

show subpopulations

African (AFR)

AF:

0.153

AC:

1571

AN:

10246

American (AMR)

AF:

0.105

AC:

3603

AN:

34446

Ashkenazi Jewish (ASJ)

AF:

0.169

AC:

1938

AN:

11498

East Asian (EAS)

AF:

0.0229

AC:

293

AN:

12800

South Asian (SAS)

AF:

0.0132

AC:

867

AN:

65900

European-Finnish (FIN)

AF:

0.0129

AC:

415

AN:

32264

Middle Eastern (MID)

AF:

0.0751

AC:

213

AN:

2838

European-Non Finnish (NFE)

AF:

0.0713

AC:

13522

AN:

189560

Other (OTH)

AF:

0.0717

AC:

1181

AN:

16468

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

947

1893

2840

3786

4733

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

240

360

480

600

<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:

0.0981

AC:

14890

AN:

151818

Hom.:

1018

Cov.:

AF XY:

0.0930

AC XY:

6900

AN XY:

74208

show subpopulations

African (AFR)

AF:

0.158

AC:

6530

AN:

41298

American (AMR)

AF:

0.127

AC:

1935

AN:

15214

Ashkenazi Jewish (ASJ)

AF:

0.177

AC:

614

AN:

3460

East Asian (EAS)

AF:

0.0163

AC:

AN:

5146

South Asian (SAS)

AF:

0.0108

AC:

AN:

4810

European-Finnish (FIN)

AF:

0.0101

AC:

107

AN:

10608

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0774

AC:

5264

AN:

67968

Other (OTH)

AF:

0.122

AC:

258

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

660

1320

1981

2641

3301

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

152

304

456

608

760

<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:

0.0845

Hom.:

2672

Bravo

AF:

0.113

Asia WGS

AF:

0.0290

AC:

102

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

(source)

DANN

Benign

0.85

PhyloP100

0.19

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