Genetic Variant ENSG00000237843:n.268+10303G>A (chr2-204485926-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000456384.1(ENSG00000237843):n.268+10303G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 151,744 control chromosomes in the GnomAD database, including 10,504 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 ( 10504 hom., cov: 32)

Consequence

ENSG00000237843
ENST00000456384.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.580

Publications

1 publications found

Variant links:

Genes affected

ENSG00000237843 (HGNC:):

ENSG00000237843 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 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
ENSG00000237843	ENST00000456384.1 link	n.268+10303G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes

AF:

0.349

AC:

52876

AN:

151624

Hom.:

10488

Cov.:

show subpopulations

Gnomad AFR

AF:

0.215

Gnomad AMI

AF:

0.310

Gnomad AMR

AF:

0.472

Gnomad ASJ

AF:

0.428

Gnomad EAS

AF:

0.810

Gnomad SAS

AF:

0.512

Gnomad FIN

AF:

0.313

Gnomad MID

AF:

0.443

Gnomad NFE

AF:

0.356

Gnomad OTH

AF:

0.362

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

GnomAD4 genome

AF:

0.349

AC:

52922

AN:

151744

Hom.:

10504

Cov.:

AF XY:

0.353

AC XY:

26182

AN XY:

74170

show subpopulations

African (AFR)

AF:

0.215

AC:

8905

AN:

41360

American (AMR)

AF:

0.473

AC:

7208

AN:

15238

Ashkenazi Jewish (ASJ)

AF:

0.428

AC:

1485

AN:

3466

East Asian (EAS)

AF:

0.810

AC:

4186

AN:

5170

South Asian (SAS)

AF:

0.514

AC:

2467

AN:

4804

European-Finnish (FIN)

AF:

0.313

AC:

3283

AN:

10480

Middle Eastern (MID)

AF:

0.439

AC:

129

AN:

294

European-Non Finnish (NFE)

AF:

0.356

AC:

24203

AN:

67912

Other (OTH)

AF:

0.367

AC:

773

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1640

3281

4921

6562

8202

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

534

1068

1602

2136

2670

<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:

0.358

Hom.:

28562

Bravo

AF:

0.357

Asia WGS

AF:

0.605

AC:

2104

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.73

(source)

DANN

Benign

0.77

PhyloP100

-0.58

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