Genetic Variant ENSG00000308733:n.93+13214A>G (chr2-135728401-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 ENST00000836082.1(ENSG00000308733):n.93+13214A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,032 control chromosomes in the GnomAD database, including 9,233 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 0.31 ( 9233 hom., cov: 32)

Consequence

ENSG00000308733
ENST00000836082.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0290

Publications

9 publications found

Variant links:

Genes affected

ENSG00000308733 (HGNC:):

ENSG00000308733 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 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
ENSG00000308733	ENST00000836082.1 link	n.93+13214A>G		intron_variant	Intron 1 of 1
ENSG00000308733	ENST00000836083.1 link	n.81+13214A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.306

AC:

46422

AN:

151914

Hom.:

9212

Cov.:

show subpopulations

Gnomad AFR

AF:

0.518

Gnomad AMI

AF:

0.140

Gnomad AMR

AF:

0.318

Gnomad ASJ

AF:

0.481

Gnomad EAS

AF:

0.500

Gnomad SAS

AF:

0.294

Gnomad FIN

AF:

0.154

Gnomad MID

AF:

0.440

Gnomad NFE

AF:

0.175

Gnomad OTH

AF:

0.343

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

GnomAD4 genome

AF:

0.306

AC:

46509

AN:

152032

Hom.:

9233

Cov.:

AF XY:

0.306

AC XY:

22736

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.518

AC:

21472

AN:

41468

American (AMR)

AF:

0.319

AC:

4862

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.481

AC:

1668

AN:

3466

East Asian (EAS)

AF:

0.501

AC:

2586

AN:

5166

South Asian (SAS)

AF:

0.295

AC:

1422

AN:

4822

European-Finnish (FIN)

AF:

0.154

AC:

1625

AN:

10570

Middle Eastern (MID)

AF:

0.449

AC:

132

AN:

294

European-Non Finnish (NFE)

AF:

0.175

AC:

11879

AN:

67958

Other (OTH)

AF:

0.348

AC:

735

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1490

2979

4469

5958

7448

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

438

876

1314

1752

2190

<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:

0.229

Hom.:

5131

Bravo

AF:

0.329

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

4.2

(source)

DANN

Benign

0.53

PhyloP100

0.029

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