ENST00000451608.2:n.*240-2339C>G – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000451608.2(ENSG00000264324):n.*240-2339C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,214 control chromosomes in the GnomAD database, including 1,611 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 0.13 ( 1611 hom., cov: 32)

Consequence

ENSG00000264324
ENST00000451608.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0260

Publications

7 publications found

Variant links:

Genes affected

ENSG00000264324 (HGNC:):

ENSG00000264324 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 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
ENSG00000264324	ENST00000451608.2 link	n.*240-2339C>G		intron_variant	Intron 6 of 38	5		ENSP00000416453.2		E7EWF7
ENSG00000301222	ENST00000777098.1 link	n.150+1214G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.126

AC:

19164

AN:

152096

Hom.:

1609

Cov.:

show subpopulations

Gnomad AFR

AF:

0.121

Gnomad AMI

AF:

0.223

Gnomad AMR

AF:

0.107

Gnomad ASJ

AF:

0.110

Gnomad EAS

AF:

0.471

Gnomad SAS

AF:

0.206

Gnomad FIN

AF:

0.102

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.105

Gnomad OTH

AF:

0.133

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

GnomAD4 genome

AF:

0.126

AC:

19171

AN:

152214

Hom.:

1611

Cov.:

AF XY:

0.129

AC XY:

9623

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.121

AC:

5013

AN:

41536

American (AMR)

AF:

0.106

AC:

1626

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.110

AC:

383

AN:

3472

East Asian (EAS)

AF:

0.471

AC:

2441

AN:

5182

South Asian (SAS)

AF:

0.207

AC:

999

AN:

4828

European-Finnish (FIN)

AF:

0.102

AC:

1079

AN:

10596

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.105

AC:

7115

AN:

68012

Other (OTH)

AF:

0.132

AC:

277

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

850

1699

2549

3398

4248

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

214

428

642

856

1070

<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:

0.107

Hom.:

132

Bravo

AF:

0.128

Asia WGS

AF:

0.330

AC:

1144

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

4.5

(source)

DANN

Benign

0.69

PhyloP100

-0.026

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over