Genetic Variant ENSG00000228714:n.229-20727T>A (chr9-115662708-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000644998.2(ENSG00000228714):n.229-20727T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 151,708 control chromosomes in the GnomAD database, including 1,124 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 ( 1124 hom., cov: 32)

Consequence

ENSG00000228714
ENST00000644998.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.636

Publications

5 publications found

Variant links:

Genes affected

ENSG00000228714 (HGNC:):

ENSG00000228714 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=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376235	XR_930270.3 link	n.145-1676A>T		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000228714	ENST00000644998.2 link	n.229-20727T>A	intron_variant	Intron 2 of 2
ENSG00000228714	ENST00000645745.1 link	n.422+26516T>A	intron_variant	Intron 4 of 5
ENSG00000228714	ENST00000646338.1 link	n.275+78754T>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.118

AC:

17812

AN:

151590

Hom.:

1127

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0788

Gnomad AMI

AF:

0.140

Gnomad AMR

AF:

0.127

Gnomad ASJ

AF:

0.113

Gnomad EAS

AF:

0.0559

Gnomad SAS

AF:

0.148

Gnomad FIN

AF:

0.116

Gnomad MID

AF:

0.156

Gnomad NFE

AF:

0.142

Gnomad OTH

AF:

0.113

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

GnomAD4 genome

AF:

0.117

AC:

17814

AN:

151708

Hom.:

1124

Cov.:

AF XY:

0.116

AC XY:

8637

AN XY:

74156

show subpopulations

African (AFR)

AF:

0.0786

AC:

3258

AN:

41442

American (AMR)

AF:

0.128

AC:

1939

AN:

15188

Ashkenazi Jewish (ASJ)

AF:

0.113

AC:

390

AN:

3460

East Asian (EAS)

AF:

0.0554

AC:

286

AN:

5160

South Asian (SAS)

AF:

0.149

AC:

716

AN:

4810

European-Finnish (FIN)

AF:

0.116

AC:

1228

AN:

10594

Middle Eastern (MID)

AF:

0.154

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.142

AC:

9591

AN:

67746

Other (OTH)

AF:

0.111

AC:

234

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

770

1540

2311

3081

3851

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:

0.128

Hom.:

166

Bravo

AF:

0.113

Asia WGS

AF:

0.111

AC:

388

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.1

(source)

DANN

Benign

0.61

PhyloP100

0.64

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