Genetic Variant ENSG00000293005:n.203-29113A>G (chr4-116225850-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.203-29113A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 152,082 control chromosomes in the GnomAD database, including 41,913 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 0.68 ( 41913 hom., cov: 31)

Consequence

ENSG00000293005
ENST00000508414.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.147

Publications

3 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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 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.203-29113A>G	intron_variant	Intron 1 of 2	3
ENSG00000293005	ENST00000509983.2 link	n.265-29113A>G	intron_variant	Intron 1 of 2	3
ENSG00000293005	ENST00000775331.1 link	n.412-29113A>G	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.685

AC:

104086

AN:

151962

Hom.:

41914

Cov.:

show subpopulations

Gnomad AFR

AF:

0.226

Gnomad AMI

AF:

0.980

Gnomad AMR

AF:

0.779

Gnomad ASJ

AF:

0.818

Gnomad EAS

AF:

0.899

Gnomad SAS

AF:

0.763

Gnomad FIN

AF:

0.921

Gnomad MID

AF:

0.712

Gnomad NFE

AF:

0.873

Gnomad OTH

AF:

0.705

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

GnomAD4 genome

AF:

0.684

AC:

104087

AN:

152082

Hom.:

41913

Cov.:

AF XY:

0.690

AC XY:

51300

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.226

AC:

9374

AN:

41470

American (AMR)

AF:

0.779

AC:

11888

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.818

AC:

2837

AN:

3468

East Asian (EAS)

AF:

0.899

AC:

4643

AN:

5162

South Asian (SAS)

AF:

0.763

AC:

3674

AN:

4814

European-Finnish (FIN)

AF:

0.921

AC:

9754

AN:

10596

Middle Eastern (MID)

AF:

0.711

AC:

209

AN:

294

European-Non Finnish (NFE)

AF:

0.873

AC:

59339

AN:

67994

Other (OTH)

AF:

0.700

AC:

1475

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1065

2131

3196

4262

5327

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

768

1536

2304

3072

3840

<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:

0.828

Hom.:

53653

Bravo

AF:

0.654

Asia WGS

AF:

0.777

AC:

2698

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

3.0

(source)

DANN

Benign

0.42

PhyloP100

0.15

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