Genetic Variant ENSG00000298930:n.468-9208T>C (chr18-78655450-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000759066.1(ENSG00000298930):n.468-9208T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 151,942 control chromosomes in the GnomAD database, including 5,772 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 0.27 ( 5772 hom., cov: 32)

Consequence

ENSG00000298930
ENST00000759066.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.26

Publications

6 publications found

Variant links:

Genes affected

ENSG00000298930 (HGNC:):

ENSG00000298930 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 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
ENSG00000298930	ENST00000759066.1 link	n.468-9208T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.272

AC:

41325

AN:

151824

Hom.:

5765

Cov.:

show subpopulations

Gnomad AFR

AF:

0.315

Gnomad AMI

AF:

0.213

Gnomad AMR

AF:

0.263

Gnomad ASJ

AF:

0.173

Gnomad EAS

AF:

0.223

Gnomad SAS

AF:

0.237

Gnomad FIN

AF:

0.269

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.262

Gnomad OTH

AF:

0.263

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

GnomAD4 genome

AF:

0.272

AC:

41367

AN:

151942

Hom.:

5772

Cov.:

AF XY:

0.272

AC XY:

20231

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.315

AC:

13035

AN:

41418

American (AMR)

AF:

0.262

AC:

4008

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.173

AC:

599

AN:

3470

East Asian (EAS)

AF:

0.222

AC:

1148

AN:

5160

South Asian (SAS)

AF:

0.238

AC:

1146

AN:

4822

European-Finnish (FIN)

AF:

0.269

AC:

2846

AN:

10562

Middle Eastern (MID)

AF:

0.197

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.262

AC:

17769

AN:

67912

Other (OTH)

AF:

0.268

AC:

564

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

1417

2834

4252

5669

7086

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

412

824

1236

1648

2060

<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:

0.272

Hom.:

1679

Bravo

AF:

0.273

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

4.7

(source)

DANN

Benign

0.29

PhyloP100

-1.3

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