Genetic Variant ENSG00000285573:n.-59T>A (chr7-36064656-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 ENST00000650410.1(ENSG00000285573):n.-59T>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,186 control chromosomes in the GnomAD database, including 1,166 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 0.11 ( 1166 hom., cov: 32)

Consequence

ENSG00000285573
ENST00000650410.1 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.308

Publications

1 publications found

Variant links:

Genes affected

ENSG00000285573 (HGNC:):

ENSG00000285573 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 (NFE) allele frequency at 95% confidence interval = 0.154 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
ENSG00000285573	ENST00000650410.1 link	n.-59T>A		upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.106

AC:

16049

AN:

152068

Hom.:

1166

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0279

Gnomad AMI

AF:

0.151

Gnomad AMR

AF:

0.0976

Gnomad ASJ

AF:

0.138

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.0369

Gnomad FIN

AF:

0.157

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.157

Gnomad OTH

AF:

0.124

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

GnomAD4 genome

AF:

0.105

AC:

16045

AN:

152186

Hom.:

1166

Cov.:

AF XY:

0.102

AC XY:

7625

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.0278

AC:

1154

AN:

41538

American (AMR)

AF:

0.0975

AC:

1491

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.138

AC:

480

AN:

3466

East Asian (EAS)

AF:

0.00116

AC:

AN:

5178

South Asian (SAS)

AF:

0.0369

AC:

178

AN:

4826

European-Finnish (FIN)

AF:

0.157

AC:

1666

AN:

10578

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.157

AC:

10643

AN:

67998

Other (OTH)

AF:

0.122

AC:

257

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

697

1394

2092

2789

3486

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

182

364

546

728

910

<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:

0.0538

Hom.:

Bravo

AF:

0.0982

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.7

(source)

DANN

Benign

0.64

PhyloP100

0.31

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