Genetic Variant ENSG00000235070:n.333-501A>G (chr2-226181626-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 ENST00000423838.2(ENSG00000235070):n.333-501A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,968 control chromosomes in the GnomAD database, including 16,445 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 0.46 ( 16445 hom., cov: 32)

Consequence

ENSG00000235070
ENST00000423838.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.209

Publications

8 publications found

Variant links:

Genes affected

ENSG00000235070 (HGNC:):

ENSG00000235070 links:

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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=-0.82).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.527 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
ENSG00000235070	ENST00000423838.2 link	n.333-501A>G	intron_variant	Intron 1 of 1	1
ENSG00000235070	ENST00000719962.1 link	n.93+3694A>G	intron_variant	Intron 1 of 1
ENSG00000235070	ENST00000719964.1 link	n.299+3694A>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.456

AC:

69293

AN:

151850

Hom.:

16427

Cov.:

show subpopulations

Gnomad AFR

AF:

0.321

Gnomad AMI

AF:

0.532

Gnomad AMR

AF:

0.471

Gnomad ASJ

AF:

0.616

Gnomad EAS

AF:

0.461

Gnomad SAS

AF:

0.545

Gnomad FIN

AF:

0.408

Gnomad MID

AF:

0.405

Gnomad NFE

AF:

0.526

Gnomad OTH

AF:

0.487

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

GnomAD4 genome

AF:

0.456

AC:

69326

AN:

151968

Hom.:

16445

Cov.:

AF XY:

0.451

AC XY:

33526

AN XY:

74268

show subpopulations

African (AFR)

AF:

0.321

AC:

13286

AN:

41446

American (AMR)

AF:

0.471

AC:

7192

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.616

AC:

2137

AN:

3468

East Asian (EAS)

AF:

0.461

AC:

2377

AN:

5152

South Asian (SAS)

AF:

0.544

AC:

2618

AN:

4812

European-Finnish (FIN)

AF:

0.408

AC:

4317

AN:

10570

Middle Eastern (MID)

AF:

0.408

AC:

120

AN:

294

European-Non Finnish (NFE)

AF:

0.526

AC:

35756

AN:

67930

Other (OTH)

AF:

0.494

AC:

1039

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1899

3799

5698

7598

9497

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

648

1296

1944

2592

3240

<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:

0.490

Hom.:

2798

Bravo

AF:

0.451

Asia WGS

AF:

0.576

AC:

2005

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

3.0

(source)

DANN

Benign

0.69

PhyloP100

0.21

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