Genetic Variant ENST00000753503.1:n.431-1383C>T (chr7-54649594-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000753503.1(ENSG00000298168):n.431-1383C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,198 control chromosomes in the GnomAD database, including 1,348 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 0.12 ( 1348 hom., cov: 33)

Consequence

ENSG00000298168
ENST00000753503.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.109

Publications

2 publications found

Variant links:

Genes affected

ENSG00000298168 (HGNC:):

ENSG00000298168 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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.17 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
ENSG00000298168	ENST00000753503.1 link	n.431-1383C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.123

AC:

18737

AN:

152080

Hom.:

1349

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0660

Gnomad AMI

AF:

0.186

Gnomad AMR

AF:

0.101

Gnomad ASJ

AF:

0.117

Gnomad EAS

AF:

0.00212

Gnomad SAS

AF:

0.112

Gnomad FIN

AF:

0.120

Gnomad MID

AF:

0.143

Gnomad NFE

AF:

0.173

Gnomad OTH

AF:

0.134

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

GnomAD4 genome

AF:

0.123

AC:

18735

AN:

152198

Hom.:

1348

Cov.:

AF XY:

0.120

AC XY:

8930

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.0659

AC:

2738

AN:

41532

American (AMR)

AF:

0.101

AC:

1542

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.117

AC:

406

AN:

3468

East Asian (EAS)

AF:

0.00213

AC:

AN:

5176

South Asian (SAS)

AF:

0.112

AC:

541

AN:

4816

European-Finnish (FIN)

AF:

0.120

AC:

1274

AN:

10596

Middle Eastern (MID)

AF:

0.140

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.173

AC:

11734

AN:

67996

Other (OTH)

AF:

0.132

AC:

278

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

840

1680

2521

3361

4201

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

216

432

648

864

1080

<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:

0.0809

Hom.:

124

Bravo

AF:

0.120

Asia WGS

AF:

0.0530

AC:

183

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.0

(source)

DANN

Benign

0.68

PhyloP100

-0.11

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