Genetic Variant ENST00000687238.1:n.832+283C>T (chr14-20441313-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000687238.1(ENSG00000291038):n.832+283C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 152,118 control chromosomes in the GnomAD database, including 9,248 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 0.35 ( 9248 hom., cov: 33)

Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

ENSG00000291038
ENST00000687238.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.11

Publications

15 publications found

Variant links:

Genes affected

ENSG00000291038 (HGNC:):

ENSG00000291038 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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000291038	ENST00000687238.1 link	n.832+283C>T	intron_variant	Intron 5 of 7
ENSG00000291038	ENST00000700970.2 link	n.610+541C>T	intron_variant	Intron 3 of 4
ENSG00000291038	ENST00000800199.1 link	n.758+541C>T	intron_variant	Intron 5 of 7

Frequencies

GnomAD3 genomes

AF:

0.345

AC:

52509

AN:

152000

Hom.:

9250

Cov.:

show subpopulations

Gnomad AFR

AF:

0.324

Gnomad AMI

AF:

0.404

Gnomad AMR

AF:

0.263

Gnomad ASJ

AF:

0.449

Gnomad EAS

AF:

0.368

Gnomad SAS

AF:

0.486

Gnomad FIN

AF:

0.426

Gnomad MID

AF:

0.465

Gnomad NFE

AF:

0.345

Gnomad OTH

AF:

0.373

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.345

AC:

52531

AN:

152116

Hom.:

9248

Cov.:

AF XY:

0.350

AC XY:

26010

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.324

AC:

13436

AN:

41468

American (AMR)

AF:

0.263

AC:

4021

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.449

AC:

1559

AN:

3470

East Asian (EAS)

AF:

0.368

AC:

1907

AN:

5176

South Asian (SAS)

AF:

0.486

AC:

2343

AN:

4824

European-Finnish (FIN)

AF:

0.426

AC:

4513

AN:

10586

Middle Eastern (MID)

AF:

0.445

AC:

129

AN:

290

European-Non Finnish (NFE)

AF:

0.345

AC:

23469

AN:

67984

Other (OTH)

AF:

0.373

AC:

786

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1812

3623

5435

7246

9058

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

536

1072

1608

2144

2680

<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:

0.350

Hom.:

16188

Bravo

AF:

0.328

Asia WGS

AF:

0.426

AC:

1482

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.70

(source)

DANN

Benign

0.47

PhyloP100

-1.1

Mutation Taster

=100/0

polymorphism

(source)

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over