Genetic Variant ENST00000755328.1:n.161+2640A>G (chr6-31206750-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+2640A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 151,956 control chromosomes in the GnomAD database, including 17,286 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 0.47 ( 17286 hom., cov: 30)

Consequence

HCG27
ENST00000755328.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.04

Publications

29 publications found

Variant links:

Genes affected

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

HCG27 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=-1.03).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.518 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+2640A>G		intron_variant	Intron 2 of 2
HCG27	ENST00000755329.1 link	n.160-1664A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.475

AC:

72084

AN:

151838

Hom.:

17273

Cov.:

show subpopulations

Gnomad AFR

AF:

0.444

Gnomad AMI

AF:

0.455

Gnomad AMR

AF:

0.528

Gnomad ASJ

AF:

0.514

Gnomad EAS

AF:

0.391

Gnomad SAS

AF:

0.406

Gnomad FIN

AF:

0.571

Gnomad MID

AF:

0.503

Gnomad NFE

AF:

0.475

Gnomad OTH

AF:

0.499

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

GnomAD4 genome

AF:

0.475

AC:

72125

AN:

151956

Hom.:

17286

Cov.:

AF XY:

0.478

AC XY:

35513

AN XY:

74258

show subpopulations

African (AFR)

AF:

0.444

AC:

18386

AN:

41450

American (AMR)

AF:

0.527

AC:

8047

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.514

AC:

1783

AN:

3468

East Asian (EAS)

AF:

0.392

AC:

2031

AN:

5176

South Asian (SAS)

AF:

0.406

AC:

1957

AN:

4824

European-Finnish (FIN)

AF:

0.571

AC:

6020

AN:

10540

Middle Eastern (MID)

AF:

0.493

AC:

145

AN:

294

European-Non Finnish (NFE)

AF:

0.475

AC:

32290

AN:

67932

Other (OTH)

AF:

0.500

AC:

1055

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1914

3827

5741

7654

9568

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

652

1304

1956

2608

3260

<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:

0.474

Hom.:

50849

Bravo

AF:

0.476

Asia WGS

AF:

0.476

AC:

1655

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.5

(source)

DANN

Benign

0.54

PhyloP100

-1.0

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