Genetic Variant ENST00000757672.1:n.224-58056A>G (chr7-86024657-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 ENST00000757672.1(ENSG00000298738):n.224-58056A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0961 in 151,940 control chromosomes in the GnomAD database, including 805 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 0.096 ( 805 hom., cov: 32)

Consequence

ENSG00000298738
ENST00000757672.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.987

Publications

2 publications found

Variant links:

Genes affected

ENSG00000298738 (HGNC:):

ENSG00000298738 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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 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
ENSG00000298738	ENST00000757672.1 link	n.224-58056A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0961

AC:

14593

AN:

151822

Hom.:

804

Cov.:

show subpopulations

Gnomad AFR

AF:

0.112

Gnomad AMI

AF:

0.109

Gnomad AMR

AF:

0.0447

Gnomad ASJ

AF:

0.0680

Gnomad EAS

AF:

0.000194

Gnomad SAS

AF:

0.0242

Gnomad FIN

AF:

0.147

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.104

Gnomad OTH

AF:

0.0732

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

GnomAD4 genome

AF:

0.0961

AC:

14604

AN:

151940

Hom.:

805

Cov.:

AF XY:

0.0952

AC XY:

7069

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.112

AC:

4661

AN:

41502

American (AMR)

AF:

0.0446

AC:

679

AN:

15224

Ashkenazi Jewish (ASJ)

AF:

0.0680

AC:

236

AN:

3472

East Asian (EAS)

AF:

0.000194

AC:

AN:

5152

South Asian (SAS)

AF:

0.0244

AC:

118

AN:

4830

European-Finnish (FIN)

AF:

0.147

AC:

1562

AN:

10592

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.104

AC:

7084

AN:

67850

Other (OTH)

AF:

0.0724

AC:

153

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

688

1375

2063

2750

3438

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

166

332

498

664

830

<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:

0.0949

Hom.:

1258

Bravo

AF:

0.0892

Asia WGS

AF:

0.0170

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

3.0

(source)

DANN

Benign

0.67

PhyloP100

-0.99

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