dbSNP rs11752262: HCP5:n.198-73A>G (chr6-31463980-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000414046.3(HCP5):n.720A>G 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 0.0907 in 527,124 control chromosomes in the GnomAD database, including 3,463 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 0.091 ( 942 hom., cov: 32)

Exomes 𝑓: 0.091 ( 2521 hom. )

Consequence

HCP5
ENST00000414046.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.00

Publications

24 publications found

Variant links:

COSMIC-nc: COSV107515454

Genes affected

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

HCP5 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000414046.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414046.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCP5	NR_040662.1		n.710A>G		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
HCP5	ENST00000541196.3	TSL:1	n.198-73A>G	intron	N/A
HCP5	ENST00000414046.3	TSL:4	n.720A>G	non_coding_transcript_exon	Exon 2 of 2
HCP5	ENST00000670109.1		n.683A>G	non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0911

AC:

13818

AN:

151730

Hom.:

941

Cov.:

show subpopulations

Gnomad AFR

AF:

0.130

Gnomad AMI

AF:

0.00989

Gnomad AMR

AF:

0.0893

Gnomad ASJ

AF:

0.0753

Gnomad EAS

AF:

0.160

Gnomad SAS

AF:

0.219

Gnomad FIN

AF:

0.0484

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.0612

Gnomad OTH

AF:

0.105

GnomAD2 exomes

AF:

0.0919

AC:

22287

AN:

242480

AF XY:

0.0966

show subpopulations

Gnomad AFR exome

AF:

0.132

Gnomad AMR exome

AF:

0.0599

Gnomad ASJ exome

AF:

0.0839

Gnomad EAS exome

AF:

0.194

Gnomad FIN exome

AF:

0.0488

Gnomad NFE exome

AF:

0.0656

Gnomad OTH exome

AF:

0.0898

GnomAD4 exome

AF:

0.0906

AC:

33996

AN:

375276

Hom.:

2521

Cov.:

AF XY:

0.100

AC XY:

21433

AN XY:

214230

show subpopulations

African (AFR)

AF:

0.135

AC:

1377

AN:

10192

American (AMR)

AF:

0.0620

AC:

2118

AN:

34140

Ashkenazi Jewish (ASJ)

AF:

0.0841

AC:

965

AN:

11472

East Asian (EAS)

AF:

0.174

AC:

2231

AN:

12792

South Asian (SAS)

AF:

0.180

AC:

11808

AN:

65778

European-Finnish (FIN)

AF:

0.0480

AC:

1548

AN:

32262

Middle Eastern (MID)

AF:

0.129

AC:

367

AN:

2836

European-Non Finnish (NFE)

AF:

0.0639

AC:

12094

AN:

189356

Other (OTH)

AF:

0.0905

AC:

1488

AN:

16448

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

1448

2897

4345

5794

7242

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

206

412

618

824

1030

<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:

0.0911

AC:

13827

AN:

151848

Hom.:

942

Cov.:

AF XY:

0.0944

AC XY:

7010

AN XY:

74248

show subpopulations

African (AFR)

AF:

0.130

AC:

5367

AN:

41310

American (AMR)

AF:

0.0892

AC:

1358

AN:

15228

Ashkenazi Jewish (ASJ)

AF:

0.0753

AC:

261

AN:

3466

East Asian (EAS)

AF:

0.160

AC:

824

AN:

5144

South Asian (SAS)

AF:

0.219

AC:

1053

AN:

4800

European-Finnish (FIN)

AF:

0.0484

AC:

513

AN:

10604

Middle Eastern (MID)

AF:

0.207

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0612

AC:

4159

AN:

67978

Other (OTH)

AF:

0.105

AC:

222

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

611

1222

1832

2443

3054

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

154

308

462

616

770

<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:

0.0725

Hom.:

2102

Bravo

AF:

0.0926

Asia WGS

AF:

0.207

AC:

717

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.3

(source)

DANN

Benign

0.23

PhyloP100

-1.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over