dbSNP rs9262632: HCG22:n.1559+121A>G (chr6-31057031-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 ENST00000426185.2(HCG22):n.1559+121A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0637 in 152,534 control chromosomes in the GnomAD database, including 398 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 0.064 ( 394 hom., cov: 32)

Exomes 𝑓: 0.097 ( 4 hom. )

Consequence

HCG22
ENST00000426185.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.28

Publications

39 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=-0.96).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCG22	NR_003948.3 link	n.1701+121A>G		intron_variant	Intron 3 of 3
HCG22	NR_145427.2 link	n.1193+121A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
HCG22	ENST00000426185.2 link	n.1559+121A>G	intron_variant	Intron 2 of 2	2
HCG22	ENST00000562344.2 link	n.1287+121A>G	intron_variant	Intron 2 of 2	5
HCG22	ENST00000565192.1 link	n.1192+121A>G	intron_variant	Intron 3 of 3	2

Frequencies

GnomAD3 genomes

AF:

0.0636

AC:

9684

AN:

152168

Hom.:

393

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0428

Gnomad AMI

AF:

0.0363

Gnomad AMR

AF:

0.0797

Gnomad ASJ

AF:

0.241

Gnomad EAS

AF:

0.0565

Gnomad SAS

AF:

0.123

Gnomad FIN

AF:

0.0531

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.0610

Gnomad OTH

AF:

0.0900

GnomAD4 exome

AF:

0.0968

AC:

AN:

248

Hom.:

AF XY:

0.0759

AC XY:

AN XY:

158

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.0500

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.125

AC:

AN:

176

Other (OTH)

AF:

0.0278

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0636

AC:

9685

AN:

152286

Hom.:

394

Cov.:

AF XY:

0.0653

AC XY:

4865

AN XY:

74456

show subpopulations

African (AFR)

AF:

0.0429

AC:

1784

AN:

41572

American (AMR)

AF:

0.0796

AC:

1217

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.241

AC:

836

AN:

3468

East Asian (EAS)

AF:

0.0567

AC:

294

AN:

5188

South Asian (SAS)

AF:

0.122

AC:

587

AN:

4824

European-Finnish (FIN)

AF:

0.0531

AC:

563

AN:

10610

Middle Eastern (MID)

AF:

0.102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0610

AC:

4150

AN:

68016

Other (OTH)

AF:

0.0905

AC:

191

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

466

932

1397

1863

2329

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

216

324

432

540

<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:

0.0663

Hom.:

1582

Bravo

AF:

0.0639

Asia WGS

AF:

0.120

AC:

416

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.21

(source)

DANN

Benign

0.27

PhyloP100

-1.3

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