Genetic Variant ENST00000690842.2:n.743-33102A>T (chr9-87330642-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 ENST00000690842.2(ENSG00000289166):n.743-33102A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,222 control chromosomes in the GnomAD database, including 2,168 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 0.16 ( 2168 hom., cov: 33)

Consequence

ENSG00000289166
ENST00000690842.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.169

Publications

3 publications found

Variant links:

Genes affected

ENSG00000289166 (HGNC:):

ENSG00000289166 links:

Genome browser will be placed here

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=-0.83).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000289166	ENST00000690842.2 link	n.743-33102A>T	intron_variant	Intron 2 of 4
ENSG00000289166	ENST00000804132.1 link	n.217-33102A>T	intron_variant	Intron 1 of 3
ENSG00000289166	ENST00000804133.1 link	n.379-33102A>T	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.158

AC:

24032

AN:

152104

Hom.:

2165

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0802

Gnomad AMI

AF:

0.322

Gnomad AMR

AF:

0.257

Gnomad ASJ

AF:

0.230

Gnomad EAS

AF:

0.232

Gnomad SAS

AF:

0.157

Gnomad FIN

AF:

0.172

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.169

Gnomad OTH

AF:

0.178

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

GnomAD4 genome

AF:

0.158

AC:

24040

AN:

152222

Hom.:

2168

Cov.:

AF XY:

0.160

AC XY:

11944

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.0801

AC:

3329

AN:

41536

American (AMR)

AF:

0.257

AC:

3935

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.230

AC:

799

AN:

3472

East Asian (EAS)

AF:

0.232

AC:

1197

AN:

5168

South Asian (SAS)

AF:

0.155

AC:

750

AN:

4828

European-Finnish (FIN)

AF:

0.172

AC:

1820

AN:

10602

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.169

AC:

11495

AN:

68010

Other (OTH)

AF:

0.178

AC:

376

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1054

2108

3161

4215

5269

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

262

524

786

1048

1310

<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:

0.163

Hom.:

298

Bravo

AF:

0.162

Asia WGS

AF:

0.193

AC:

668

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

5.6

(source)

DANN

Benign

0.77

PhyloP100

-0.17

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