dbSNP rs8080616: ENSG00000286356:n.186+32672G>T (chr17-5739998-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 ENST00000783338.1(ENSG00000286356):n.186+32672G>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 0.0021 ( 8 hom., cov: 27)

Failed GnomAD Quality Control

Consequence

ENSG00000286356
ENST00000783338.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.03

Publications

1 publications found

Variant links:

Genes affected

ENSG00000286356 (HGNC:):

ENSG00000286356 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=-0.96).

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
ENSG00000286356	ENST00000783338.1 link	n.186+32672G>T		intron_variant	Intron 1 of 1
ENSG00000286356	ENST00000783339.1 link	n.174-20653G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.00215

AC:

310

AN:

144374

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000491

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000615

Gnomad ASJ

AF:

0.00674

Gnomad EAS

AF:

0.000843

Gnomad SAS

AF:

0.0296

Gnomad FIN

AF:

0.000914

Gnomad MID

AF:

0.0166

Gnomad NFE

AF:

0.00154

Gnomad OTH

AF:

0.00297

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: AS_VQSR

AF:

0.00213

AC:

308

AN:

144446

Hom.:

Cov.:

AF XY:

0.00259

AC XY:

181

AN XY:

69952

show subpopulations

African (AFR)

AF:

0.000490

AC:

AN:

38796

American (AMR)

AF:

0.000615

AC:

AN:

14640

Ashkenazi Jewish (ASJ)

AF:

0.00674

AC:

AN:

3412

East Asian (EAS)

AF:

0.000846

AC:

AN:

4728

South Asian (SAS)

AF:

0.0294

AC:

133

AN:

4518

European-Finnish (FIN)

AF:

0.000914

AC:

AN:

8754

Middle Eastern (MID)

AF:

0.0180

AC:

AN:

278

European-Non Finnish (NFE)

AF:

0.00152

AC:

101

AN:

66406

Other (OTH)

AF:

0.00294

AC:

AN:

2042

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.572

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<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:

0.00335

Hom.:

634

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.49

(source)

DANN

Benign

0.34

PhyloP100

-1.0

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