Genetic Variant ENST00000638546.2:n.36G>A (chr6-31197750-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 ENST00000638546.2(HCG27):n.36G>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 0.127 in 454,262 control chromosomes in the GnomAD database, including 4,128 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 0.12 ( 1236 hom., cov: 32)

Exomes 𝑓: 0.13 ( 2892 hom. )

Consequence

HCG27
ENST00000638546.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.182

Publications

14 publications found

Variant links:

COSMIC-nc: COSV67271546

Genes affected

HCG27 (HGNC:27366): (HLA complex group 27)

HCG27 links:

ENSG00000272501 (HGNC:):

ENSG00000272501 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=-0.75).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCG27	NR_026791.1 link	n.-10G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
HCG27	ENST00000638546.2 link	n.36G>A	non_coding_transcript_exon_variant	Exon 1 of 2	1
ENSG00000272501	ENST00000606367.1 link	n.288C>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000272501	ENST00000755443.1 link	n.182+24C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.122

AC:

18574

AN:

152020

Hom.:

1234

Cov.:

show subpopulations

Gnomad AFR

AF:

0.103

Gnomad AMI

AF:

0.187

Gnomad AMR

AF:

0.155

Gnomad ASJ

AF:

0.170

Gnomad EAS

AF:

0.109

Gnomad SAS

AF:

0.139

Gnomad FIN

AF:

0.184

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.111

Gnomad OTH

AF:

0.173

GnomAD2 exomes

AF:

0.140

AC:

18145

AN:

129684

AF XY:

0.139

show subpopulations

Gnomad AFR exome

AF:

0.106

Gnomad AMR exome

AF:

0.190

Gnomad ASJ exome

AF:

0.175

Gnomad EAS exome

AF:

0.140

Gnomad FIN exome

AF:

0.164

Gnomad NFE exome

AF:

0.110

Gnomad OTH exome

AF:

0.139

GnomAD4 exome

AF:

0.130

AC:

39224

AN:

302124

Hom.:

2892

Cov.:

AF XY:

0.131

AC XY:

22545

AN XY:

171912

show subpopulations

African (AFR)

AF:

0.105

AC:

906

AN:

8590

American (AMR)

AF:

0.191

AC:

5194

AN:

27146

Ashkenazi Jewish (ASJ)

AF:

0.173

AC:

1864

AN:

10748

East Asian (EAS)

AF:

0.131

AC:

1201

AN:

9168

South Asian (SAS)

AF:

0.147

AC:

8794

AN:

59658

European-Finnish (FIN)

AF:

0.159

AC:

1967

AN:

12336

Middle Eastern (MID)

AF:

0.171

AC:

474

AN:

2772

European-Non Finnish (NFE)

AF:

0.108

AC:

17083

AN:

157586

Other (OTH)

AF:

0.123

AC:

1741

AN:

14120

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.442

Heterozygous variant carriers

1635

3270

4905

6540

8175

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

176

352

528

704

880

<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:

0.122

AC:

18597

AN:

152138

Hom.:

1236

Cov.:

AF XY:

0.126

AC XY:

9392

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.103

AC:

4296

AN:

41520

American (AMR)

AF:

0.155

AC:

2374

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.170

AC:

588

AN:

3466

East Asian (EAS)

AF:

0.109

AC:

563

AN:

5170

South Asian (SAS)

AF:

0.139

AC:

671

AN:

4816

European-Finnish (FIN)

AF:

0.184

AC:

1951

AN:

10584

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.111

AC:

7559

AN:

67986

Other (OTH)

AF:

0.173

AC:

365

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

810

1620

2430

3240

4050

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome 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

Alfa

AF:

0.122

Hom.:

1124

Bravo

AF:

0.122

Asia WGS

AF:

0.134

AC:

465

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

9.2

(source)

DANN

Uncertain

0.98

PhyloP100

0.18

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