Genetic Variant ENST00000557251.1:n.167-9211A>T (chr14-42693894-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000557251.1(ENSG00000258394):n.167-9211A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 152,004 control chromosomes in the GnomAD database, including 37,712 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 0.70 ( 37712 hom., cov: 32)

Consequence

ENSG00000258394
ENST00000557251.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.641

Publications

1 publications found

Variant links:

Genes affected

ENSG00000258394 (HGNC:):

ENSG00000258394 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 (NFE) allele frequency at 95% confidence interval = 0.762 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
ENSG00000258394	ENST00000557251.1 link	n.167-9211A>T		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes

AF:

0.698

AC:

105984

AN:

151886

Hom.:

37687

Cov.:

show subpopulations

Gnomad AFR

AF:

0.571

Gnomad AMI

AF:

0.783

Gnomad AMR

AF:

0.717

Gnomad ASJ

AF:

0.679

Gnomad EAS

AF:

0.554

Gnomad SAS

AF:

0.647

Gnomad FIN

AF:

0.806

Gnomad MID

AF:

0.696

Gnomad NFE

AF:

0.767

Gnomad OTH

AF:

0.717

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

GnomAD4 genome

AF:

0.698

AC:

106063

AN:

152004

Hom.:

37712

Cov.:

AF XY:

0.699

AC XY:

51913

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.571

AC:

23670

AN:

41422

American (AMR)

AF:

0.718

AC:

10953

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.679

AC:

2355

AN:

3466

East Asian (EAS)

AF:

0.553

AC:

2857

AN:

5164

South Asian (SAS)

AF:

0.648

AC:

3121

AN:

4818

European-Finnish (FIN)

AF:

0.806

AC:

8523

AN:

10572

Middle Eastern (MID)

AF:

0.690

AC:

203

AN:

294

European-Non Finnish (NFE)

AF:

0.767

AC:

52146

AN:

67980

Other (OTH)

AF:

0.719

AC:

1521

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1588

3176

4763

6351

7939

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

826

1652

2478

3304

4130

<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:

0.739

Hom.:

5253

Bravo

AF:

0.683

Asia WGS

AF:

0.647

AC:

2253

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

2.9

(source)

DANN

Benign

0.67

PhyloP100

0.64

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