Genetic Variant ENST00000717053.1:n.288-8778C>T (chr1-181844414-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000717053.1(ENSG00000287452):n.288-8778C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,116 control chromosomes in the GnomAD database, including 1,511 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 0.10 ( 1511 hom., cov: 33)

Consequence

ENSG00000287452
ENST00000717053.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.664

Publications

3 publications found

Variant links:

Genes affected

ENSG00000287452 (HGNC:):

ENSG00000287452 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=-0.67).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000287452	ENST00000717053.1 link	n.288-8778C>T	intron_variant	Intron 1 of 3
ENSG00000287452	ENST00000717054.1 link	n.293-8778C>T	intron_variant	Intron 1 of 3
ENSG00000287452	ENST00000717055.1 link	n.81-8778C>T	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15840

AN:

151998

Hom.:

1508

Cov.:

show subpopulations

Gnomad AFR

AF:

0.232

Gnomad AMI

AF:

0.145

Gnomad AMR

AF:

0.0807

Gnomad ASJ

AF:

0.0472

Gnomad EAS

AF:

0.264

Gnomad SAS

AF:

0.0756

Gnomad FIN

AF:

0.0289

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0361

Gnomad OTH

AF:

0.0886

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

GnomAD4 genome

AF:

0.104

AC:

15860

AN:

152116

Hom.:

1511

Cov.:

AF XY:

0.104

AC XY:

7738

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.232

AC:

9638

AN:

41482

American (AMR)

AF:

0.0805

AC:

1231

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0472

AC:

164

AN:

3472

East Asian (EAS)

AF:

0.265

AC:

1367

AN:

5164

South Asian (SAS)

AF:

0.0759

AC:

366

AN:

4822

European-Finnish (FIN)

AF:

0.0289

AC:

306

AN:

10578

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0361

AC:

2458

AN:

67996

Other (OTH)

AF:

0.0872

AC:

184

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

669

1338

2007

2676

3345

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

320

480

640

800

<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:

0.0515

Hom.:

1077

Bravo

AF:

0.115

Asia WGS

AF:

0.157

AC:

549

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

8.0

(source)

DANN

Benign

0.84

PhyloP100

0.66

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