Genetic Variant ENSG00000293005:n.203-35857A>G (chr4-116232594-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 ENST00000508414.5(ENSG00000293005):n.203-35857A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.891 in 151,998 control chromosomes in the GnomAD database, including 62,352 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 0.89 ( 62352 hom., cov: 32)

Consequence

ENSG00000293005
ENST00000508414.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.349

Publications

1 publications found

Variant links:

Genes affected

ENSG00000293005 (HGNC:):

ENSG00000293005 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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000293005	ENST00000508414.5 link	n.203-35857A>G	intron_variant	Intron 1 of 2	3
ENSG00000293005	ENST00000509983.2 link	n.265-35857A>G	intron_variant	Intron 1 of 2	3
ENSG00000293005	ENST00000775331.1 link	n.412-35857A>G	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.891

AC:

135392

AN:

151880

Hom.:

62325

Cov.:

show subpopulations

Gnomad AFR

AF:

0.635

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.954

Gnomad ASJ

AF:

0.987

Gnomad EAS

AF:

0.997

Gnomad SAS

AF:

0.957

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.908

Gnomad NFE

AF:

0.997

Gnomad OTH

AF:

0.921

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

GnomAD4 genome

AF:

0.891

AC:

135464

AN:

151998

Hom.:

62352

Cov.:

AF XY:

0.893

AC XY:

66385

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.635

AC:

26277

AN:

41410

American (AMR)

AF:

0.954

AC:

14528

AN:

15234

Ashkenazi Jewish (ASJ)

AF:

0.987

AC:

3426

AN:

3472

East Asian (EAS)

AF:

0.997

AC:

5151

AN:

5164

South Asian (SAS)

AF:

0.957

AC:

4618

AN:

4824

European-Finnish (FIN)

AF:

1.00

AC:

10606

AN:

10606

Middle Eastern (MID)

AF:

0.911

AC:

266

AN:

292

European-Non Finnish (NFE)

AF:

0.997

AC:

67742

AN:

67974

Other (OTH)

AF:

0.919

AC:

1940

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

556

1112

1668

2224

2780

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

882

1764

2646

3528

4410

<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:

0.936

Hom.:

7970

Bravo

AF:

0.876

Asia WGS

AF:

0.943

AC:

3264

AN:

3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.8

(source)

DANN

Benign

0.64

PhyloP100

-0.35

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