Genetic Variant ENST00000835213.1:n.-208T>C (chr17-13140986-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000835213.1(ENSG00000308590):n.-208T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 151,960 control chromosomes in the GnomAD database, including 10,645 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 0.37 ( 10645 hom., cov: 32)

Consequence

ENSG00000308590
ENST00000835213.1 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.470

Publications

5 publications found

Variant links:

Genes affected

ENSG00000308590 (HGNC:):

ENSG00000308590 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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect
ENSG00000308590	ENST00000835213.1 link	n.-208T>C	upstream_gene_variant
ENSG00000308590	ENST00000835214.1 link	n.-227T>C	upstream_gene_variant
ENSG00000308590	ENST00000835215.1 link	n.-240T>C	upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.370

AC:

56188

AN:

151842

Hom.:

10632

Cov.:

show subpopulations

Gnomad AFR

AF:

0.303

Gnomad AMI

AF:

0.315

Gnomad AMR

AF:

0.334

Gnomad ASJ

AF:

0.301

Gnomad EAS

AF:

0.374

Gnomad SAS

AF:

0.529

Gnomad FIN

AF:

0.412

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.405

Gnomad OTH

AF:

0.375

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

GnomAD4 genome

AF:

0.370

AC:

56220

AN:

151960

Hom.:

10645

Cov.:

AF XY:

0.373

AC XY:

27702

AN XY:

74262

show subpopulations

African (AFR)

AF:

0.304

AC:

12584

AN:

41450

American (AMR)

AF:

0.333

AC:

5096

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.301

AC:

1044

AN:

3466

East Asian (EAS)

AF:

0.374

AC:

1927

AN:

5152

South Asian (SAS)

AF:

0.528

AC:

2541

AN:

4808

European-Finnish (FIN)

AF:

0.412

AC:

4360

AN:

10570

Middle Eastern (MID)

AF:

0.374

AC:

110

AN:

294

European-Non Finnish (NFE)

AF:

0.405

AC:

27486

AN:

67912

Other (OTH)

AF:

0.373

AC:

786

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1776

3552

5328

7104

8880

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

566

1132

1698

2264

2830

<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:

0.388

Hom.:

38223

Bravo

AF:

0.356

Asia WGS

AF:

0.463

AC:

1606

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

7.6

(source)

DANN

Benign

0.46

PhyloP100

0.47

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