dbSNP rs2523840: HCG22:n.734-1361G>A (chr6-31062648-G-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.734-1361G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 151,994 control chromosomes in the GnomAD database, including 3,645 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 0.21 ( 3645 hom., cov: 32)

Consequence

HCG22
ENST00000805383.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0120

Publications

16 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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.348 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.734-1361G>A	intron_variant	Intron 2 of 2
HCG22	ENST00000805384.1 link	n.554-1361G>A	intron_variant	Intron 2 of 2
HCG22	ENST00000805385.1 link	n.460-1361G>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.208

AC:

31562

AN:

151876

Hom.:

3637

Cov.:

show subpopulations

Gnomad AFR

AF:

0.275

Gnomad AMI

AF:

0.0835

Gnomad AMR

AF:

0.210

Gnomad ASJ

AF:

0.425

Gnomad EAS

AF:

0.281

Gnomad SAS

AF:

0.360

Gnomad FIN

AF:

0.133

Gnomad MID

AF:

0.242

Gnomad NFE

AF:

0.151

Gnomad OTH

AF:

0.239

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

GnomAD4 genome

AF:

0.208

AC:

31598

AN:

151994

Hom.:

3645

Cov.:

AF XY:

0.211

AC XY:

15651

AN XY:

74284

show subpopulations

African (AFR)

AF:

0.275

AC:

11406

AN:

41444

American (AMR)

AF:

0.210

AC:

3208

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.425

AC:

1474

AN:

3468

East Asian (EAS)

AF:

0.281

AC:

1454

AN:

5174

South Asian (SAS)

AF:

0.362

AC:

1745

AN:

4820

European-Finnish (FIN)

AF:

0.133

AC:

1400

AN:

10550

Middle Eastern (MID)

AF:

0.243

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.151

AC:

10263

AN:

67974

Other (OTH)

AF:

0.237

AC:

501

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

1229

2458

3688

4917

6146

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

340

680

1020

1360

1700

<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:

0.176

Hom.:

5299

Bravo

AF:

0.213

Asia WGS

AF:

0.334

AC:

1162

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.8

(source)

DANN

Benign

0.61

PhyloP100

-0.012

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