Genetic Variant ENSG00000286046:n.419-3211T>G (chr4-18625889-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000652661.1(ENSG00000286046):n.419-3211T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0407 in 152,258 control chromosomes in the GnomAD database, including 239 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 0.041 ( 239 hom., cov: 33)

Consequence

ENSG00000286046
ENST00000652661.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.49

Publications

1 publications found

Variant links:

Genes affected

ENSG00000286046 (HGNC:):

ENSG00000286046 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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105374510	XR_001741601.2 link	n.823-3211T>G	intron_variant	Intron 2 of 6
LOC105374510	XR_001741602.2 link	n.91-3211T>G	intron_variant	Intron 1 of 5
LOC105374510	XR_925445.3 link	n.433-3211T>G	intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286046	ENST00000652661.1 link	n.419-3211T>G		intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes

AF:

0.0406

AC:

6177

AN:

152140

Hom.:

235

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0695

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.0907

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.123

Gnomad SAS

AF:

0.0781

Gnomad FIN

AF:

0.0312

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.00685

Gnomad OTH

AF:

0.0379

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

GnomAD4 genome

AF:

0.0407

AC:

6201

AN:

152258

Hom.:

239

Cov.:

AF XY:

0.0439

AC XY:

3265

AN XY:

74452

show subpopulations

African (AFR)

AF:

0.0694

AC:

2883

AN:

41542

American (AMR)

AF:

0.0914

AC:

1398

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.00202

AC:

AN:

3470

East Asian (EAS)

AF:

0.122

AC:

635

AN:

5186

South Asian (SAS)

AF:

0.0786

AC:

379

AN:

4824

European-Finnish (FIN)

AF:

0.0312

AC:

331

AN:

10614

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00685

AC:

466

AN:

68012

Other (OTH)

AF:

0.0403

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

271

542

813

1084

1355

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

136

204

272

340

<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:

0.0195

Hom.:

119

Bravo

AF:

0.0450

Asia WGS

AF:

0.121

AC:

420

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.8

(source)

DANN

Benign

0.44

PhyloP100

1.5

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