dbSNP rs3129763: ENSG00000309733:n.-25C>T (chr6-32623148-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 ENST00000843606.1(ENSG00000309733):n.-25C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,132 control chromosomes in the GnomAD database, including 4,398 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 0.23 ( 4398 hom., cov: 33)

Consequence

ENSG00000309733
ENST00000843606.1 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.60

Publications

80 publications found

Variant links:

Genes affected

ENSG00000309733 (HGNC:):

ENSG00000309733 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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 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
ENSG00000309733	ENST00000843606.1 link	n.-25C>T		upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.232

AC:

35282

AN:

152014

Hom.:

4395

Cov.:

show subpopulations

Gnomad AFR

AF:

0.245

Gnomad AMI

AF:

0.167

Gnomad AMR

AF:

0.243

Gnomad ASJ

AF:

0.277

Gnomad EAS

AF:

0.149

Gnomad SAS

AF:

0.205

Gnomad FIN

AF:

0.159

Gnomad MID

AF:

0.396

Gnomad NFE

AF:

0.239

Gnomad OTH

AF:

0.252

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

GnomAD4 genome

AF:

0.232

AC:

35303

AN:

152132

Hom.:

4398

Cov.:

AF XY:

0.228

AC XY:

16942

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.245

AC:

10150

AN:

41462

American (AMR)

AF:

0.243

AC:

3709

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.277

AC:

961

AN:

3470

East Asian (EAS)

AF:

0.148

AC:

770

AN:

5188

South Asian (SAS)

AF:

0.205

AC:

989

AN:

4822

European-Finnish (FIN)

AF:

0.159

AC:

1686

AN:

10592

Middle Eastern (MID)

AF:

0.405

AC:

119

AN:

294

European-Non Finnish (NFE)

AF:

0.239

AC:

16237

AN:

67990

Other (OTH)

AF:

0.251

AC:

530

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1358

2715

4073

5430

6788

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

382

764

1146

1528

1910

<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:

0.243

Hom.:

13495

Bravo

AF:

0.238

Asia WGS

AF:

0.167

AC:

580

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.0

(source)

DANN

Benign

0.45

PhyloP100

-1.6

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