Genetic Variant ENST00000426882.6:n.797+8819C>G (chr6-30317535-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000426882.6(HCG18):n.797+8819C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.06 in 152,212 control chromosomes in the GnomAD database, including 460 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 0.060 ( 460 hom., cov: 32)

Consequence

HCG18
ENST00000426882.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0470

Publications

16 publications found

Variant links:

Genes affected

HCG18 (HGNC:31337): (HLA complex group 18)

HCG18 links:

HCG17 (HGNC:31339): (HLA complex group 17)

HCG17 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=-0.95).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
HCG18	NR_024052.2 link	n.804-3053C>G	intron_variant	Intron 1 of 4
HCG18	NR_024053.2 link	n.803+8819C>G	intron_variant	Intron 1 of 3
HCG17	NR_052012.1 link	n.126+8474C>G	intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
HCG18	ENST00000426882.6 link	n.797+8819C>G	intron_variant	Intron 1 of 2	1
HCG18	ENST00000412685.10 link	n.533+8819C>G	intron_variant	Intron 1 of 2	2
HCG18	ENST00000413358.6 link	n.39-3053C>G	intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.0601

AC:

9139

AN:

152094

Hom.:

460

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0149

Gnomad AMI

AF:

0.170

Gnomad AMR

AF:

0.0238

Gnomad ASJ

AF:

0.0302

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.000208

Gnomad FIN

AF:

0.0695

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.104

Gnomad OTH

AF:

0.0379

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0600

AC:

9136

AN:

152212

Hom.:

460

Cov.:

AF XY:

0.0548

AC XY:

4080

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.0149

AC:

617

AN:

41544

American (AMR)

AF:

0.0237

AC:

363

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0302

AC:

105

AN:

3472

East Asian (EAS)

AF:

0.000193

AC:

AN:

5188

South Asian (SAS)

AF:

0.000208

AC:

AN:

4812

European-Finnish (FIN)

AF:

0.0695

AC:

736

AN:

10594

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.104

AC:

7078

AN:

67998

Other (OTH)

AF:

0.0375

AC:

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

427

854

1280

1707

2134

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

110

220

330

440

550

<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:

0.0459

Hom.:

Bravo

AF:

0.0552

Asia WGS

AF:

0.00346

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

3.5

(source)

DANN

Benign

0.50

PhyloP100

0.047

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over