Genetic Variant ENSG00000291175:n.134+2583G>T (chr17-45581989-C-A) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000686949.1(ENSG00000291175):n.134+2583G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.43 ( 2209 hom., cov: 56)

Failed GnomAD Quality Control

Consequence

ENSG00000291175
ENST00000686949.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.216

Publications

3 publications found

Variant links:

Genes affected

ENSG00000291175 (HGNC:):

ENSG00000291175 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000291175	ENST00000686949.1 link	n.134+2583G>T	intron_variant	Intron 1 of 7
ENSG00000291175	ENST00000701132.2 link	n.134+2583G>T	intron_variant	Intron 1 of 2
ENSG00000291175	ENST00000717223.1 link	n.560+3713G>T	intron_variant	Intron 1 of 9

Frequencies

GnomAD3 genomes

AF:

0.435

AC:

65693

AN:

150980

Hom.:

2211

Cov.:

show subpopulations

Gnomad AFR

AF:

0.328

Gnomad AMI

AF:

0.513

Gnomad AMR

AF:

0.448

Gnomad ASJ

AF:

0.508

Gnomad EAS

AF:

0.317

Gnomad SAS

AF:

0.469

Gnomad FIN

AF:

0.429

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.498

Gnomad OTH

AF:

0.470

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

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.435

AC:

65705

AN:

151096

Hom.:

2209

Cov.:

AF XY:

0.431

AC XY:

31835

AN XY:

73848

show subpopulations

African (AFR)

AF:

0.327

AC:

13440

AN:

41050

American (AMR)

AF:

0.447

AC:

6787

AN:

15174

Ashkenazi Jewish (ASJ)

AF:

0.508

AC:

1758

AN:

3464

East Asian (EAS)

AF:

0.317

AC:

1620

AN:

5114

South Asian (SAS)

AF:

0.469

AC:

2252

AN:

4800

European-Finnish (FIN)

AF:

0.429

AC:

4482

AN:

10456

Middle Eastern (MID)

AF:

0.503

AC:

148

AN:

294

European-Non Finnish (NFE)

AF:

0.498

AC:

33767

AN:

67738

Other (OTH)

AF:

0.469

AC:

985

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.537

Heterozygous variant carriers

1382

2764

4146

5528

6910

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.351

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

1.1

(source)

DANN

Benign

0.33

PhyloP100

-0.22

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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17-45581989-C-A

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