Genetic Variant ENSG00000286605:n.528-7114T>G (chr18-30405513-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 ENST00000657542.1(ENSG00000286605):n.528-7114T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0304 in 152,296 control chromosomes in the GnomAD database, including 91 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 0.030 ( 91 hom., cov: 33)

Consequence

ENSG00000286605
ENST00000657542.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.255

Publications

2 publications found

Variant links:

Genes affected

ENSG00000286605 (HGNC:):

ENSG00000286605 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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0797 is higher than 0.05.

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
ENSG00000286605	ENST00000657542.1 link	n.528-7114T>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0304

AC:

4629

AN:

152178

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0144

Gnomad AMI

AF:

0.0482

Gnomad AMR

AF:

0.0484

Gnomad ASJ

AF:

0.0179

Gnomad EAS

AF:

0.0865

Gnomad SAS

AF:

0.0546

Gnomad FIN

AF:

0.0238

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0313

Gnomad OTH

AF:

0.0401

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

GnomAD4 genome

AF:

0.0304

AC:

4623

AN:

152296

Hom.:

Cov.:

AF XY:

0.0306

AC XY:

2281

AN XY:

74462

show subpopulations

African (AFR)

AF:

0.0143

AC:

596

AN:

41574

American (AMR)

AF:

0.0483

AC:

738

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0179

AC:

AN:

3470

East Asian (EAS)

AF:

0.0863

AC:

448

AN:

5190

South Asian (SAS)

AF:

0.0543

AC:

262

AN:

4828

European-Finnish (FIN)

AF:

0.0238

AC:

253

AN:

10622

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0313

AC:

2129

AN:

68008

Other (OTH)

AF:

0.0402

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

229

459

688

918

1147

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

174

232

290

<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:

0.00961

Hom.:

Bravo

AF:

0.0322

Asia WGS

AF:

0.0880

AC:

306

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.2

(source)

DANN

Benign

0.65

PhyloP100

0.26

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