Genetic Variant HCG9:n.147G>A (chr6-29975258-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000376800.7(HCG9):n.147G>A 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 0.193 in 531,894 control chromosomes in the GnomAD database, including 11,249 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 0.22 ( 4183 hom., cov: 30)

Exomes 𝑓: 0.18 ( 7066 hom. )

Consequence

HCG9
ENST00000376800.7 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.324

Publications

29 publications found

Variant links:

COSMIC-nc: COSV65136404

Genes affected

HCG9 (HGNC:21243): (HLA complex group 9) This gene lies within the MHC class I region on chromosome 6p21.3. This gene is believed to be non-coding, but its function has not been determined. [provided by RefSeq, Jul 2009]

HCG9 links:

MICD (HGNC:7093): (MHC class I polypeptide-related sequence D (pseudogene))

MICD links:

POLR1HASP (HGNC:):

POLR1HASP 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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCG9	NR_028032.1 link	n.144G>A		non_coding_transcript_exon_variant	Exon 1 of 3
MICD		n.29975258G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
HCG9	ENST00000376800.7 link	n.147G>A	non_coding_transcript_exon_variant	Exon 1 of 3	1
POLR1HASP	ENST00000849678.1 link	n.589-28342C>T	intron_variant	Intron 3 of 4
POLR1HASP	ENST00000849679.1 link	n.65+1345C>T	intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.219

AC:

33277

AN:

151712

Hom.:

4164

Cov.:

show subpopulations

Gnomad AFR

AF:

0.331

Gnomad AMI

AF:

0.114

Gnomad AMR

AF:

0.278

Gnomad ASJ

AF:

0.193

Gnomad EAS

AF:

0.142

Gnomad SAS

AF:

0.237

Gnomad FIN

AF:

0.126

Gnomad MID

AF:

0.213

Gnomad NFE

AF:

0.160

Gnomad OTH

AF:

0.243

GnomAD2 exomes

AF:

0.186

AC:

44828

AN:

240778

AF XY:

0.182

show subpopulations

Gnomad AFR exome

AF:

0.317

Gnomad AMR exome

AF:

0.276

Gnomad ASJ exome

AF:

0.190

Gnomad EAS exome

AF:

0.160

Gnomad FIN exome

AF:

0.125

Gnomad NFE exome

AF:

0.149

Gnomad OTH exome

AF:

0.187

GnomAD4 exome

AF:

0.182

AC:

69331

AN:

380064

Hom.:

7066

Cov.:

AF XY:

0.184

AC XY:

39770

AN XY:

216256

show subpopulations

African (AFR)

AF:

0.322

AC:

3386

AN:

10502

American (AMR)

AF:

0.277

AC:

9870

AN:

35586

Ashkenazi Jewish (ASJ)

AF:

0.192

AC:

2244

AN:

11714

East Asian (EAS)

AF:

0.175

AC:

2322

AN:

13302

South Asian (SAS)

AF:

0.229

AC:

15171

AN:

66176

European-Finnish (FIN)

AF:

0.129

AC:

4041

AN:

31306

Middle Eastern (MID)

AF:

0.193

AC:

550

AN:

2846

European-Non Finnish (NFE)

AF:

0.150

AC:

28706

AN:

191936

Other (OTH)

AF:

0.182

AC:

3041

AN:

16696

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.424

Heterozygous variant carriers

3370

6740

10110

13480

16850

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

394

788

1182

1576

1970

<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:

0.220

AC:

33352

AN:

151830

Hom.:

4183

Cov.:

AF XY:

0.218

AC XY:

16169

AN XY:

74200

show subpopulations

African (AFR)

AF:

0.331

AC:

13682

AN:

41342

American (AMR)

AF:

0.278

AC:

4247

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.193

AC:

671

AN:

3468

East Asian (EAS)

AF:

0.142

AC:

730

AN:

5126

South Asian (SAS)

AF:

0.239

AC:

1151

AN:

4816

European-Finnish (FIN)

AF:

0.126

AC:

1330

AN:

10580

Middle Eastern (MID)

AF:

0.223

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.160

AC:

10858

AN:

67920

Other (OTH)

AF:

0.244

AC:

514

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

1205

2409

3614

4818

6023

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

344

688

1032

1376

1720

<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:

0.185

Hom.:

10230

Bravo

AF:

0.238

Asia WGS

AF:

0.216

AC:

748

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

5.1

(source)

DANN

Benign

0.60

PhyloP100

-0.32

Splicing

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

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over