Genetic Variant HCG18:n.410-2091T>C (chr6-30225736-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 ENST00000844410.1(HCG18):n.410-2091T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 152,092 control chromosomes in the GnomAD database, including 13,668 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 0.42 ( 13668 hom., cov: 32)

Consequence

HCG18
ENST00000844410.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.778

Publications

14 publications found

Variant links:

Genes affected

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

HCG18 links:

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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=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCG18	ENST00000844410.1 link	n.410-2091T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.421

AC:

64026

AN:

151972

Hom.:

13641

Cov.:

show subpopulations

Gnomad AFR

AF:

0.406

Gnomad AMI

AF:

0.510

Gnomad AMR

AF:

0.410

Gnomad ASJ

AF:

0.364

Gnomad EAS

AF:

0.310

Gnomad SAS

AF:

0.393

Gnomad FIN

AF:

0.416

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.447

Gnomad OTH

AF:

0.388

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

GnomAD4 genome

AF:

0.421

AC:

64106

AN:

152092

Hom.:

13668

Cov.:

AF XY:

0.418

AC XY:

31064

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.407

AC:

16867

AN:

41470

American (AMR)

AF:

0.411

AC:

6274

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.364

AC:

1264

AN:

3468

East Asian (EAS)

AF:

0.310

AC:

1604

AN:

5170

South Asian (SAS)

AF:

0.395

AC:

1903

AN:

4822

European-Finnish (FIN)

AF:

0.416

AC:

4397

AN:

10582

Middle Eastern (MID)

AF:

0.316

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.447

AC:

30418

AN:

67982

Other (OTH)

AF:

0.389

AC:

822

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1892

3783

5675

7566

9458

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.431

Hom.:

26872

Bravo

AF:

0.420

Asia WGS

AF:

0.371

AC:

1290

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.3

(source)

DANN

Benign

0.70

PhyloP100

-0.78

Splicing

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

Publications

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6-30225736-A-G

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