Genetic Variant ENST00000807481.1:n.518-28G>T (chr14-43334278-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000807481.1(ENSG00000304974):n.518-28G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,152 control chromosomes in the GnomAD database, including 1,781 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 ( 1781 hom., cov: 33)

Consequence

ENSG00000304974
ENST00000807481.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.240

Publications

1 publications found

Variant links:

Genes affected

ENSG00000304974 (HGNC:):

ENSG00000304974 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903307	XR_007064136.1 link	n.205-1518C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000304974	ENST00000807481.1 link	n.518-28G>T	intron_variant	Intron 2 of 3
ENSG00000304974	ENST00000807482.1 link	n.627-28G>T	intron_variant	Intron 2 of 5
ENSG00000304974	ENST00000807483.1 link	n.363-28G>T	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.134

AC:

20351

AN:

152034

Hom.:

1768

Cov.:

show subpopulations

Gnomad AFR

AF:

0.187

Gnomad AMI

AF:

0.112

Gnomad AMR

AF:

0.224

Gnomad ASJ

AF:

0.149

Gnomad EAS

AF:

0.341

Gnomad SAS

AF:

0.114

Gnomad FIN

AF:

0.103

Gnomad MID

AF:

0.137

Gnomad NFE

AF:

0.0718

Gnomad OTH

AF:

0.126

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

GnomAD4 genome

AF:

0.134

AC:

20400

AN:

152152

Hom.:

1781

Cov.:

AF XY:

0.139

AC XY:

10360

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.187

AC:

7764

AN:

41500

American (AMR)

AF:

0.224

AC:

3422

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.149

AC:

518

AN:

3470

East Asian (EAS)

AF:

0.341

AC:

1757

AN:

5156

South Asian (SAS)

AF:

0.114

AC:

548

AN:

4824

European-Finnish (FIN)

AF:

0.103

AC:

1087

AN:

10604

Middle Eastern (MID)

AF:

0.134

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0718

AC:

4881

AN:

67998

Other (OTH)

AF:

0.134

AC:

282

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

873

1746

2619

3492

4365

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

210

420

630

840

1050

<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:

0.0960

Hom.:

505

Bravo

AF:

0.149

Asia WGS

AF:

0.264

AC:

917

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.2

(source)

DANN

Benign

0.74

PhyloP100

-0.24

Splicing

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