Genetic Variant ENST00000805383.1:n.733+1597C>A (chr6-31061396-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000805383.1(HCG22):n.733+1597C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,074 control chromosomes in the GnomAD database, including 3,859 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 ( 3859 hom., cov: 32)

Consequence

HCG22
ENST00000805383.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.454

Publications

9 publications found

Variant links:

Genes affected

HCG22 (HGNC:27780): (HLA complex group 22 (non-protein coding)) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

HCG22 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=-0.91).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
HCG22	ENST00000805383.1 link	n.733+1597C>A	intron_variant	Intron 2 of 2
HCG22	ENST00000805384.1 link	n.553+1597C>A	intron_variant	Intron 2 of 2
HCG22	ENST00000805385.1 link	n.459+1613C>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.223

AC:

33902

AN:

151956

Hom.:

3861

Cov.:

show subpopulations

Gnomad AFR

AF:

0.186

Gnomad AMI

AF:

0.299

Gnomad AMR

AF:

0.252

Gnomad ASJ

AF:

0.202

Gnomad EAS

AF:

0.191

Gnomad SAS

AF:

0.220

Gnomad FIN

AF:

0.292

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.230

Gnomad OTH

AF:

0.238

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

GnomAD4 genome

AF:

0.223

AC:

33904

AN:

152074

Hom.:

3859

Cov.:

AF XY:

0.224

AC XY:

16658

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.186

AC:

7733

AN:

41504

American (AMR)

AF:

0.252

AC:

3846

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.202

AC:

702

AN:

3470

East Asian (EAS)

AF:

0.191

AC:

987

AN:

5160

South Asian (SAS)

AF:

0.219

AC:

1057

AN:

4822

European-Finnish (FIN)

AF:

0.292

AC:

3081

AN:

10548

Middle Eastern (MID)

AF:

0.282

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.230

AC:

15644

AN:

67994

Other (OTH)

AF:

0.236

AC:

498

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1355

2710

4064

5419

6774

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

356

712

1068

1424

1780

<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:

0.230

Hom.:

3623

Bravo

AF:

0.219

Asia WGS

AF:

0.175

AC:

611

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.0

(source)

DANN

Benign

0.62

PhyloP100

0.45

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