dbSNP rs2517506: HCG22:n.734-106T>C (chr6-31063903-T-C) – 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.734-106T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,246 control chromosomes in the GnomAD database, including 3,741 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 ( 3741 hom., cov: 33)

Consequence

HCG22
ENST00000805383.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.371

Publications

14 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 (SAS) allele frequency at 95% confidence interval = 0.351 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.734-106T>C	intron_variant	Intron 2 of 2
HCG22	ENST00000805384.1 link	n.554-106T>C	intron_variant	Intron 2 of 2
HCG22	ENST00000805385.1 link	n.460-106T>C	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.211

AC:

32026

AN:

152128

Hom.:

3733

Cov.:

show subpopulations

Gnomad AFR

AF:

0.276

Gnomad AMI

AF:

0.0899

Gnomad AMR

AF:

0.214

Gnomad ASJ

AF:

0.438

Gnomad EAS

AF:

0.280

Gnomad SAS

AF:

0.364

Gnomad FIN

AF:

0.136

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.154

Gnomad OTH

AF:

0.246

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

GnomAD4 genome

AF:

0.211

AC:

32061

AN:

152246

Hom.:

3741

Cov.:

AF XY:

0.213

AC XY:

15886

AN XY:

74434

show subpopulations

African (AFR)

AF:

0.276

AC:

11450

AN:

41514

American (AMR)

AF:

0.214

AC:

3275

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.438

AC:

1521

AN:

3472

East Asian (EAS)

AF:

0.281

AC:

1453

AN:

5176

South Asian (SAS)

AF:

0.365

AC:

1763

AN:

4824

European-Finnish (FIN)

AF:

0.136

AC:

1442

AN:

10610

Middle Eastern (MID)

AF:

0.259

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.154

AC:

10482

AN:

68026

Other (OTH)

AF:

0.245

AC:

517

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1311

2623

3934

5246

6557

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

346

692

1038

1384

1730

<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:

0.194

Hom.:

1473

Bravo

AF:

0.215

Asia WGS

AF:

0.339

AC:

1177

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

2.1

(source)

DANN

Benign

0.43

PhyloP100

-0.37

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