Genetic Variant HCG27:n.161+1209A>G (chr6-31205319-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 ENST00000755328.1(HCG27):n.161+1209A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,178 control chromosomes in the GnomAD database, including 1,218 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 0.12 ( 1218 hom., cov: 32)

Consequence

HCG27
ENST00000755328.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.199

Publications

14 publications found

Variant links:

Genes affected

HCG27 (HGNC:27366): (HLA complex group 27)

HCG27 links:

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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=-0.92).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCG27	ENST00000755328.1 link	n.161+1209A>G		intron_variant	Intron 2 of 2
HCG27	ENST00000755329.1 link	n.159+1209A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.121

AC:

18399

AN:

152060

Hom.:

1216

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0981

Gnomad AMI

AF:

0.188

Gnomad AMR

AF:

0.155

Gnomad ASJ

AF:

0.171

Gnomad EAS

AF:

0.109

Gnomad SAS

AF:

0.139

Gnomad FIN

AF:

0.185

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.112

Gnomad OTH

AF:

0.170

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

GnomAD4 genome

AF:

0.121

AC:

18420

AN:

152178

Hom.:

1218

Cov.:

AF XY:

0.125

AC XY:

9313

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.0982

AC:

4074

AN:

41498

American (AMR)

AF:

0.155

AC:

2371

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.171

AC:

592

AN:

3470

East Asian (EAS)

AF:

0.109

AC:

567

AN:

5182

South Asian (SAS)

AF:

0.139

AC:

672

AN:

4826

European-Finnish (FIN)

AF:

0.185

AC:

1963

AN:

10598

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.112

AC:

7593

AN:

68004

Other (OTH)

AF:

0.170

AC:

358

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

830

1660

2491

3321

4151

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

206

412

618

824

1030

<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:

0.122

Hom.:

1110

Bravo

AF:

0.120

Asia WGS

AF:

0.134

AC:

465

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

5.0

(source)

DANN

Benign

0.29

PhyloP100

0.20

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