Genetic Variant ENSG00000235435:n.126+11121T>G (chr2-145314285-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000454965.1(ENSG00000235435):n.126+11121T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,064 control chromosomes in the GnomAD database, including 5,220 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 0.25 ( 5220 hom., cov: 32)

Consequence

ENSG00000235435
ENST00000454965.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0130

Publications

11 publications found

Variant links:

Genes affected

ENSG00000235435 (HGNC:):

ENSG00000235435 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=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.301 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
ENSG00000235435	ENST00000454965.1 link	n.126+11121T>G	intron_variant	Intron 3 of 4	3
ENSG00000309192	ENST00000839437.1 link	n.54-21653A>C	intron_variant	Intron 1 of 2
ENSG00000309192	ENST00000839438.1 link	n.54-21653A>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.250

AC:

37998

AN:

151946

Hom.:

5221

Cov.:

show subpopulations

Gnomad AFR

AF:

0.149

Gnomad AMI

AF:

0.213

Gnomad AMR

AF:

0.272

Gnomad ASJ

AF:

0.338

Gnomad EAS

AF:

0.121

Gnomad SAS

AF:

0.308

Gnomad FIN

AF:

0.267

Gnomad MID

AF:

0.347

Gnomad NFE

AF:

0.305

Gnomad OTH

AF:

0.262

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

GnomAD4 genome

AF:

0.250

AC:

37991

AN:

152064

Hom.:

5220

Cov.:

AF XY:

0.249

AC XY:

18508

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.149

AC:

6190

AN:

41498

American (AMR)

AF:

0.272

AC:

4148

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.338

AC:

1173

AN:

3468

East Asian (EAS)

AF:

0.120

AC:

622

AN:

5164

South Asian (SAS)

AF:

0.307

AC:

1477

AN:

4814

European-Finnish (FIN)

AF:

0.267

AC:

2829

AN:

10588

Middle Eastern (MID)

AF:

0.342

AC:

100

AN:

292

European-Non Finnish (NFE)

AF:

0.305

AC:

20707

AN:

67968

Other (OTH)

AF:

0.262

AC:

552

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1406

2813

4219

5626

7032

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

386

772

1158

1544

1930

<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:

0.284

Hom.:

18030

Bravo

AF:

0.243

Asia WGS

AF:

0.214

AC:

745

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.1

(source)

DANN

Benign

0.43

PhyloP100

-0.013

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