dbSNP rs12281017: ENSG00000301530:n.138+13852G>A (chr11-69210034-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000779509.1(ENSG00000301530):n.138+13852G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,244 control chromosomes in the GnomAD database, including 2,270 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 0.16 ( 2270 hom., cov: 33)

Consequence

ENSG00000301530
ENST00000779509.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.95

Publications

9 publications found

Variant links:

Genes affected

ENSG00000301530 (HGNC:):

ENSG00000301530 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=-0.96).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.208 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
ENSG00000301530	ENST00000779509.1 link	n.138+13852G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.162

AC:

24645

AN:

152126

Hom.:

2271

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0896

Gnomad AMI

AF:

0.138

Gnomad AMR

AF:

0.144

Gnomad ASJ

AF:

0.278

Gnomad EAS

AF:

0.0505

Gnomad SAS

AF:

0.196

Gnomad FIN

AF:

0.150

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.211

Gnomad OTH

AF:

0.196

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

GnomAD4 genome

AF:

0.162

AC:

24630

AN:

152244

Hom.:

2270

Cov.:

AF XY:

0.160

AC XY:

11918

AN XY:

74438

show subpopulations

African (AFR)

AF:

0.0895

AC:

3720

AN:

41554

American (AMR)

AF:

0.144

AC:

2198

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.278

AC:

963

AN:

3464

East Asian (EAS)

AF:

0.0494

AC:

256

AN:

5178

South Asian (SAS)

AF:

0.195

AC:

942

AN:

4820

European-Finnish (FIN)

AF:

0.150

AC:

1596

AN:

10616

Middle Eastern (MID)

AF:

0.293

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.211

AC:

14336

AN:

67990

Other (OTH)

AF:

0.192

AC:

407

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1081

2162

3243

4324

5405

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

274

548

822

1096

1370

<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:

0.198

Hom.:

3739

Bravo

AF:

0.157

Asia WGS

AF:

0.120

AC:

419

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.21

(source)

DANN

Benign

0.54

PhyloP100

-1.9

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