Genetic Variant ENST00000762706.1:n.306-469T>C (chr2-112770329-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 ENST00000762706.1(ENSG00000299339):n.306-469T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 151,992 control chromosomes in the GnomAD database, including 7,951 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 0.32 ( 7951 hom., cov: 32)

Consequence

ENSG00000299339
ENST00000762706.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.366

Publications

15 publications found

Variant links:

Genes affected

ENSG00000299339 (HGNC:):

ENSG00000299339 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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000299339	ENST00000762706.1 link	n.306-469T>C	intron_variant	Intron 1 of 3
ENSG00000299339	ENST00000762707.1 link	n.401-469T>C	intron_variant	Intron 1 of 2
ENSG00000299339	ENST00000762708.1 link	n.167-469T>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.317

AC:

48096

AN:

151876

Hom.:

7928

Cov.:

show subpopulations

Gnomad AFR

AF:

0.389

Gnomad AMI

AF:

0.408

Gnomad AMR

AF:

0.292

Gnomad ASJ

AF:

0.343

Gnomad EAS

AF:

0.0799

Gnomad SAS

AF:

0.300

Gnomad FIN

AF:

0.316

Gnomad MID

AF:

0.377

Gnomad NFE

AF:

0.295

Gnomad OTH

AF:

0.308

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

GnomAD4 genome

AF:

0.317

AC:

48161

AN:

151992

Hom.:

7951

Cov.:

AF XY:

0.316

AC XY:

23499

AN XY:

74280

show subpopulations

African (AFR)

AF:

0.389

AC:

16138

AN:

41444

American (AMR)

AF:

0.291

AC:

4452

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.343

AC:

1189

AN:

3470

East Asian (EAS)

AF:

0.0799

AC:

414

AN:

5182

South Asian (SAS)

AF:

0.300

AC:

1446

AN:

4814

European-Finnish (FIN)

AF:

0.316

AC:

3323

AN:

10530

Middle Eastern (MID)

AF:

0.374

AC:

110

AN:

294

European-Non Finnish (NFE)

AF:

0.295

AC:

20072

AN:

67960

Other (OTH)

AF:

0.306

AC:

647

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1642

3285

4927

6570

8212

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

474

948

1422

1896

2370

<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:

0.302

Hom.:

22199

Bravo

AF:

0.315

Asia WGS

AF:

0.214

AC:

749

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

3.6

(source)

DANN

Benign

0.55

PhyloP100

-0.37

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