Genetic Variant ENSG00000301321:n.221+7326A>G (chr11-130485336-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000777947.1(ENSG00000301321):n.221+7326A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,162 control chromosomes in the GnomAD database, including 4,942 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 ( 4942 hom., cov: 33)

Consequence

ENSG00000301321
ENST00000777947.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.811

Publications

0 publications found

Variant links:

Genes affected

ENSG00000301321 (HGNC:):

ENSG00000301321 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=-0.85).

BA1

GnomAd4 highest subpopulation (SAS) 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	Effect	Exon rank
ENSG00000301321	ENST00000777947.1 link	n.221+7326A>G	intron_variant	Intron 2 of 3
ENSG00000301321	ENST00000777948.1 link	n.431+7326A>G	intron_variant	Intron 2 of 3
ENSG00000301321	ENST00000777949.1 link	n.560+6602A>G	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.249

AC:

37800

AN:

152044

Hom.:

4928

Cov.:

show subpopulations

Gnomad AFR

AF:

0.276

Gnomad AMI

AF:

0.216

Gnomad AMR

AF:

0.188

Gnomad ASJ

AF:

0.266

Gnomad EAS

AF:

0.172

Gnomad SAS

AF:

0.370

Gnomad FIN

AF:

0.264

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.240

Gnomad OTH

AF:

0.245

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

GnomAD4 genome

AF:

0.249

AC:

37844

AN:

152162

Hom.:

4942

Cov.:

AF XY:

0.249

AC XY:

18527

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.277

AC:

11485

AN:

41502

American (AMR)

AF:

0.188

AC:

2870

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.266

AC:

923

AN:

3470

East Asian (EAS)

AF:

0.171

AC:

886

AN:

5178

South Asian (SAS)

AF:

0.370

AC:

1782

AN:

4822

European-Finnish (FIN)

AF:

0.264

AC:

2802

AN:

10594

Middle Eastern (MID)

AF:

0.279

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.240

AC:

16304

AN:

67988

Other (OTH)

AF:

0.243

AC:

513

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1462

2925

4387

5850

7312

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

410

820

1230

1640

2050

<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:

0.242

Hom.:

566

Bravo

AF:

0.240

Asia WGS

AF:

0.254

AC:

882

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.5

(source)

DANN

Benign

0.79

PhyloP100

0.81

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