Genetic Variant ENSG00000259130:n.346+12441A>G (chr14-20965183-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 ENST00000717680.1(ENSG00000259130):n.346+12441A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 152,156 control chromosomes in the GnomAD database, including 39,539 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 0.72 ( 39539 hom., cov: 33)

Consequence

ENSG00000259130
ENST00000717680.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.571

Publications

9 publications found

Variant links:

Genes affected

ENSG00000259130 (HGNC:):

ENSG00000259130 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000259130	ENST00000717680.1 link	n.346+12441A>G	intron_variant	Intron 2 of 3
ENSG00000259130	ENST00000796665.1 link	n.772+6423A>G	intron_variant	Intron 3 of 4
ENSG00000259130	ENST00000796666.1 link	n.267+6423A>G	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.719

AC:

109273

AN:

152038

Hom.:

39502

Cov.:

show subpopulations

Gnomad AFR

AF:

0.704

Gnomad AMI

AF:

0.850

Gnomad AMR

AF:

0.760

Gnomad ASJ

AF:

0.708

Gnomad EAS

AF:

0.859

Gnomad SAS

AF:

0.843

Gnomad FIN

AF:

0.777

Gnomad MID

AF:

0.718

Gnomad NFE

AF:

0.689

Gnomad OTH

AF:

0.708

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

GnomAD4 genome

AF:

0.719

AC:

109365

AN:

152156

Hom.:

39539

Cov.:

AF XY:

0.726

AC XY:

54002

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.704

AC:

29238

AN:

41508

American (AMR)

AF:

0.761

AC:

11648

AN:

15308

Ashkenazi Jewish (ASJ)

AF:

0.708

AC:

2456

AN:

3468

East Asian (EAS)

AF:

0.859

AC:

4435

AN:

5164

South Asian (SAS)

AF:

0.842

AC:

4061

AN:

4822

European-Finnish (FIN)

AF:

0.777

AC:

8233

AN:

10600

Middle Eastern (MID)

AF:

0.718

AC:

211

AN:

294

European-Non Finnish (NFE)

AF:

0.689

AC:

46816

AN:

67968

Other (OTH)

AF:

0.706

AC:

1492

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1611

3223

4834

6446

8057

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

846

1692

2538

3384

4230

<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:

0.709

Hom.:

32505

Bravo

AF:

0.718

Asia WGS

AF:

0.811

AC:

2819

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

7.4

(source)

DANN

Benign

0.71

PhyloP100

0.57

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