dbSNP rs12422521: ENSG00000308331:n.628+3300T>C (chr12-131375817-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 ENST00000833340.1(ENSG00000308331):n.628+3300T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,120 control chromosomes in the GnomAD database, including 1,498 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 0.12 ( 1498 hom., cov: 33)

Consequence

ENSG00000308331
ENST00000833340.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.644

Publications

1 publications found

Variant links:

Genes affected

ENSG00000308331 (HGNC:):

ENSG00000308331 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=-1.23).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 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
ENSG00000308331	ENST00000833340.1 link	n.628+3300T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.122

AC:

18570

AN:

152002

Hom.:

1495

Cov.:

show subpopulations

Gnomad AFR

AF:

0.229

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.0733

Gnomad ASJ

AF:

0.0795

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.0677

Gnomad FIN

AF:

0.0975

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.0894

Gnomad OTH

AF:

0.111

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

GnomAD4 genome

AF:

0.122

AC:

18592

AN:

152120

Hom.:

1498

Cov.:

AF XY:

0.119

AC XY:

8881

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.228

AC:

9479

AN:

41490

American (AMR)

AF:

0.0732

AC:

1119

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0795

AC:

276

AN:

3470

East Asian (EAS)

AF:

0.00116

AC:

AN:

5174

South Asian (SAS)

AF:

0.0688

AC:

331

AN:

4812

European-Finnish (FIN)

AF:

0.0975

AC:

1033

AN:

10592

Middle Eastern (MID)

AF:

0.105

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0894

AC:

6079

AN:

67978

Other (OTH)

AF:

0.110

AC:

231

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

812

1624

2437

3249

4061

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

194

388

582

776

970

<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:

0.0969

Hom.:

417

Bravo

AF:

0.125

Asia WGS

AF:

0.0400

AC:

142

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.2

CADD

Benign

4.4

(source)

DANN

Benign

0.71

PhyloP100

0.64

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