Genetic Variant ENST00000686949.1:n.134+10427G>C (chr17-45574145-C-G) – 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+10427G>C 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 ( 2173 hom., cov: 51)

Failed GnomAD Quality Control

Consequence

ENSG00000291175
ENST00000686949.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.109

Publications

4 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=-0.93).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000686949.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
ENSG00000291175	ENST00000686949.1	n.134+10427G>C	intron	N/A
ENSG00000291175	ENST00000701132.2	n.134+10427G>C	intron	N/A
ENSG00000291175	ENST00000717223.1	n.560+11557G>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.435

AC:

65658

AN:

151046

Hom.:

2175

Cov.:

show subpopulations

Gnomad AFR

AF:

0.328

Gnomad AMI

AF:

0.513

Gnomad AMR

AF:

0.447

Gnomad ASJ

AF:

0.507

Gnomad EAS

AF:

0.317

Gnomad SAS

AF:

0.467

Gnomad FIN

AF:

0.429

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.498

Gnomad OTH

AF:

0.469

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:

0.434

AC:

65673

AN:

151166

Hom.:

2173

Cov.:

AF XY:

0.431

AC XY:

31804

AN XY:

73846

show subpopulations

African (AFR)

AF:

0.327

AC:

13443

AN:

41076

American (AMR)

AF:

0.447

AC:

6762

AN:

15132

Ashkenazi Jewish (ASJ)

AF:

0.507

AC:

1757

AN:

3464

East Asian (EAS)

AF:

0.317

AC:

1618

AN:

5110

South Asian (SAS)

AF:

0.467

AC:

2242

AN:

4802

European-Finnish (FIN)

AF:

0.429

AC:

4495

AN:

10486

Middle Eastern (MID)

AF:

0.503

AC:

146

AN:

290

European-Non Finnish (NFE)

AF:

0.498

AC:

33762

AN:

67800

Other (OTH)

AF:

0.468

AC:

981

AN:

2096

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

1695

3391

5086

6782

8477

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

776

1552

2328

3104

3880

<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:

0.457

Hom.:

299

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.86

(source)

DANN

Benign

0.43

PhyloP100

-0.11

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over