Genetic Variant ENSG00000302327:n.1289-17328A>G (chr2-36324684-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 ENST00000785824.1(ENSG00000302327):n.1289-17328A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,014 control chromosomes in the GnomAD database, including 7,174 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 0.30 ( 7174 hom., cov: 32)

Consequence

ENSG00000302327
ENST00000785824.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.364

Publications

3 publications found

Variant links:

Genes affected

ENSG00000302327 (HGNC:):

ENSG00000302327 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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 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
ENSG00000302327	ENST00000785824.1 link	n.1289-17328A>G		intron_variant	Intron 1 of 1
ENSG00000302327	ENST00000785825.1 link	n.306-2582A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.298

AC:

45209

AN:

151894

Hom.:

7149

Cov.:

show subpopulations

Gnomad AFR

AF:

0.359

Gnomad AMI

AF:

0.400

Gnomad AMR

AF:

0.217

Gnomad ASJ

AF:

0.168

Gnomad EAS

AF:

0.263

Gnomad SAS

AF:

0.182

Gnomad FIN

AF:

0.386

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.283

Gnomad OTH

AF:

0.252

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

GnomAD4 genome

AF:

0.298

AC:

45274

AN:

152014

Hom.:

7174

Cov.:

AF XY:

0.296

AC XY:

22010

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.359

AC:

14899

AN:

41450

American (AMR)

AF:

0.217

AC:

3315

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.168

AC:

583

AN:

3468

East Asian (EAS)

AF:

0.262

AC:

1354

AN:

5160

South Asian (SAS)

AF:

0.182

AC:

877

AN:

4824

European-Finnish (FIN)

AF:

0.386

AC:

4075

AN:

10556

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.283

AC:

19231

AN:

67960

Other (OTH)

AF:

0.257

AC:

543

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1565

3130

4696

6261

7826

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

450

900

1350

1800

2250

<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:

0.273

Hom.:

5713

Bravo

AF:

0.291

Asia WGS

AF:

0.231

AC:

805

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

2.0

(source)

DANN

Benign

0.52

PhyloP100

-0.36

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