Genetic Variant HCG22:n.734-1664T>G (chr6-31062345-T-G) – 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.734-1664T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,948 control chromosomes in the GnomAD database, including 15,705 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 0.45 ( 15705 hom., cov: 31)

Consequence

HCG22
ENST00000805383.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.620

Publications

28 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=-0.95).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.573 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.734-1664T>G	intron_variant	Intron 2 of 2
HCG22	ENST00000805384.1 link	n.554-1664T>G	intron_variant	Intron 2 of 2
HCG22	ENST00000805385.1 link	n.460-1664T>G	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.450

AC:

68336

AN:

151830

Hom.:

15689

Cov.:

show subpopulations

Gnomad AFR

AF:

0.507

Gnomad AMI

AF:

0.400

Gnomad AMR

AF:

0.480

Gnomad ASJ

AF:

0.643

Gnomad EAS

AF:

0.471

Gnomad SAS

AF:

0.590

Gnomad FIN

AF:

0.429

Gnomad MID

AF:

0.585

Gnomad NFE

AF:

0.389

Gnomad OTH

AF:

0.510

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

GnomAD4 genome

AF:

0.450

AC:

68384

AN:

151948

Hom.:

15705

Cov.:

AF XY:

0.453

AC XY:

33654

AN XY:

74264

show subpopulations

African (AFR)

AF:

0.507

AC:

20993

AN:

41418

American (AMR)

AF:

0.480

AC:

7318

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.643

AC:

2228

AN:

3466

East Asian (EAS)

AF:

0.472

AC:

2434

AN:

5158

South Asian (SAS)

AF:

0.591

AC:

2847

AN:

4814

European-Finnish (FIN)

AF:

0.429

AC:

4533

AN:

10558

Middle Eastern (MID)

AF:

0.575

AC:

169

AN:

294

European-Non Finnish (NFE)

AF:

0.389

AC:

26431

AN:

67962

Other (OTH)

AF:

0.506

AC:

1068

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1903

3806

5708

7611

9514

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

632

1264

1896

2528

3160

<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:

0.420

Hom.:

32244

Bravo

AF:

0.453

Asia WGS

AF:

0.522

AC:

1818

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

0.77

(source)

DANN

Benign

0.79

PhyloP100

-0.62

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