Genetic Variant ENSG00000282564:n.242-13006T>A (chr1-230563488-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000685406.1(ENSG00000282564):n.242-13006T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,230 control chromosomes in the GnomAD database, including 1,565 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 0.13 ( 1565 hom., cov: 32)

Consequence

ENSG00000282564
ENST00000685406.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.177

Publications

2 publications found

Variant links:

Genes affected

ENSG00000282564 (HGNC:):

ENSG00000282564 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985357	XR_007066934.1 link	n.171-7127A>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000282564	ENST00000685406.1 link	n.242-13006T>A	intron_variant	Intron 2 of 5
ENSG00000282564	ENST00000689608.2 link	n.330-55475T>A	intron_variant	Intron 2 of 3
ENSG00000282564	ENST00000692577.3 link	n.319-55475T>A	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.130

AC:

19768

AN:

152114

Hom.:

1566

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0972

Gnomad AMI

AF:

0.0559

Gnomad AMR

AF:

0.128

Gnomad ASJ

AF:

0.105

Gnomad EAS

AF:

0.387

Gnomad SAS

AF:

0.249

Gnomad FIN

AF:

0.0623

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.134

Gnomad OTH

AF:

0.142

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

GnomAD4 genome

AF:

0.130

AC:

19766

AN:

152230

Hom.:

1565

Cov.:

AF XY:

0.129

AC XY:

9635

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.0970

AC:

4031

AN:

41544

American (AMR)

AF:

0.128

AC:

1957

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.105

AC:

366

AN:

3472

East Asian (EAS)

AF:

0.388

AC:

2008

AN:

5172

South Asian (SAS)

AF:

0.249

AC:

1197

AN:

4816

European-Finnish (FIN)

AF:

0.0623

AC:

661

AN:

10614

Middle Eastern (MID)

AF:

0.252

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.134

AC:

9116

AN:

68006

Other (OTH)

AF:

0.144

AC:

305

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

881

1761

2642

3522

4403

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

232

464

696

928

1160

<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:

0.126

Hom.:

144

Bravo

AF:

0.132

Asia WGS

AF:

0.317

AC:

1099

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

3.5

(source)

DANN

Benign

0.69

PhyloP100

0.18

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