Genetic Variant ENSG00000298738:n.224-15708T>C (chr7-85982309-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000757672.1(ENSG00000298738):n.224-15708T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 151,716 control chromosomes in the GnomAD database, including 27,256 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 0.57 ( 27256 hom., cov: 30)

Consequence

ENSG00000298738
ENST00000757672.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.03

Publications

5 publications found

Variant links:

Genes affected

ENSG00000298738 (HGNC:):

ENSG00000298738 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000757672.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757672.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298738	ENST00000757672.1		n.224-15708T>C		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.573

AC:

86883

AN:

151596

Hom.:

27199

Cov.:

show subpopulations

Gnomad AFR

AF:

0.840

Gnomad AMI

AF:

0.712

Gnomad AMR

AF:

0.474

Gnomad ASJ

AF:

0.514

Gnomad EAS

AF:

0.356

Gnomad SAS

AF:

0.374

Gnomad FIN

AF:

0.496

Gnomad MID

AF:

0.653

Gnomad NFE

AF:

0.476

Gnomad OTH

AF:

0.560

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

GnomAD4 genome

AF:

0.573

AC:

86996

AN:

151716

Hom.:

27256

Cov.:

AF XY:

0.566

AC XY:

42003

AN XY:

74146

show subpopulations

African (AFR)

AF:

0.841

AC:

34807

AN:

41406

American (AMR)

AF:

0.474

AC:

7193

AN:

15178

Ashkenazi Jewish (ASJ)

AF:

0.514

AC:

1779

AN:

3464

East Asian (EAS)

AF:

0.357

AC:

1839

AN:

5150

South Asian (SAS)

AF:

0.375

AC:

1806

AN:

4814

European-Finnish (FIN)

AF:

0.496

AC:

5222

AN:

10530

Middle Eastern (MID)

AF:

0.656

AC:

193

AN:

294

European-Non Finnish (NFE)

AF:

0.476

AC:

32333

AN:

67862

Other (OTH)

AF:

0.558

AC:

1175

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1614

3229

4843

6458

8072

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

704

1408

2112

2816

3520

<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:

0.491

Hom.:

7625

Bravo

AF:

0.588

Asia WGS

AF:

0.418

AC:

1452

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.36

(source)

DANN

Benign

0.38

PhyloP100

-2.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over