Genetic Variant ENST00000754979.1:n.114-3466A>G (chr17-18074612-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000754979.1(ENSG00000298337):n.114-3466A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 151,898 control chromosomes in the GnomAD database, including 13,040 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 0.40 ( 13040 hom., cov: 31)

Consequence

ENSG00000298337
ENST00000754979.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.80

Publications

6 publications found

Variant links:

Genes affected

ENSG00000298337 (HGNC:):

ENSG00000298337 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 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
ENSG00000298337	ENST00000754979.1 link	n.114-3466A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.400

AC:

60753

AN:

151780

Hom.:

13021

Cov.:

show subpopulations

Gnomad AFR

AF:

0.430

Gnomad AMI

AF:

0.417

Gnomad AMR

AF:

0.453

Gnomad ASJ

AF:

0.405

Gnomad EAS

AF:

0.757

Gnomad SAS

AF:

0.708

Gnomad FIN

AF:

0.408

Gnomad MID

AF:

0.373

Gnomad NFE

AF:

0.320

Gnomad OTH

AF:

0.394

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

GnomAD4 genome

AF:

0.400

AC:

60808

AN:

151898

Hom.:

13040

Cov.:

AF XY:

0.412

AC XY:

30611

AN XY:

74240

show subpopulations

African (AFR)

AF:

0.430

AC:

17820

AN:

41416

American (AMR)

AF:

0.454

AC:

6921

AN:

15236

Ashkenazi Jewish (ASJ)

AF:

0.405

AC:

1403

AN:

3466

East Asian (EAS)

AF:

0.758

AC:

3915

AN:

5166

South Asian (SAS)

AF:

0.707

AC:

3405

AN:

4814

European-Finnish (FIN)

AF:

0.408

AC:

4308

AN:

10556

Middle Eastern (MID)

AF:

0.378

AC:

111

AN:

294

European-Non Finnish (NFE)

AF:

0.320

AC:

21714

AN:

67932

Other (OTH)

AF:

0.395

AC:

831

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1719

3438

5156

6875

8594

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

584

1168

1752

2336

2920

<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:

0.370

Hom.:

2247

Bravo

AF:

0.402

Asia WGS

AF:

0.679

AC:

2358

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.60

(source)

DANN

Benign

0.55

PhyloP100

-1.8

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