Genetic Variant ENSG00000253227:n.297+4607T>C (chr8-124281001-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 ENST00000739901.1(ENSG00000253227):n.297+4607T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 152,100 control chromosomes in the GnomAD database, including 33,161 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 0.66 ( 33161 hom., cov: 33)

Consequence

ENSG00000253227
ENST00000739901.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.135

Publications

8 publications found

Variant links:

Genes affected

ENSG00000253227 (HGNC:58365):

ENSG00000253227 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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 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
ENSG00000253227	ENST00000739901.1 link	n.297+4607T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.660

AC:

100289

AN:

151982

Hom.:

33116

Cov.:

show subpopulations

Gnomad AFR

AF:

0.665

Gnomad AMI

AF:

0.702

Gnomad AMR

AF:

0.695

Gnomad ASJ

AF:

0.738

Gnomad EAS

AF:

0.748

Gnomad SAS

AF:

0.651

Gnomad FIN

AF:

0.596

Gnomad MID

AF:

0.646

Gnomad NFE

AF:

0.648

Gnomad OTH

AF:

0.667

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

GnomAD4 genome

AF:

0.660

AC:

100382

AN:

152100

Hom.:

33161

Cov.:

AF XY:

0.659

AC XY:

49005

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.665

AC:

27580

AN:

41478

American (AMR)

AF:

0.695

AC:

10623

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.738

AC:

2561

AN:

3472

East Asian (EAS)

AF:

0.749

AC:

3869

AN:

5168

South Asian (SAS)

AF:

0.654

AC:

3157

AN:

4830

European-Finnish (FIN)

AF:

0.596

AC:

6300

AN:

10568

Middle Eastern (MID)

AF:

0.653

AC:

192

AN:

294

European-Non Finnish (NFE)

AF:

0.648

AC:

44046

AN:

67978

Other (OTH)

AF:

0.670

AC:

1414

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1809

3618

5427

7236

9045

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

800

1600

2400

3200

4000

<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:

0.660

Hom.:

132337

Bravo

AF:

0.671

Asia WGS

AF:

0.695

AC:

2414

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

(source)

DANN

Benign

0.79

PhyloP100

-0.14

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