dbSNP rs9469300: ENSG00000289559:n.1731C>T (chr6-32892975-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 ENST00000688327.3(ENSG00000289559):n.1731C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,072 control chromosomes in the GnomAD database, including 1,457 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 0.13 ( 1457 hom., cov: 32)

Consequence

ENSG00000289559
ENST00000688327.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.457

Publications

24 publications found

Variant links:

Genes affected

ENSG00000289559 (HGNC:):

ENSG00000289559 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 = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000289559	ENST00000688327.3 link	n.1731C>T	non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000289559	ENST00000753352.1 link	n.856+612C>T	intron_variant	Intron 2 of 2
ENSG00000289559	ENST00000753353.1 link	n.507+612C>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.129

AC:

19598

AN:

151956

Hom.:

1451

Cov.:

show subpopulations

Gnomad AFR

AF:

0.193

Gnomad AMI

AF:

0.0746

Gnomad AMR

AF:

0.0954

Gnomad ASJ

AF:

0.185

Gnomad EAS

AF:

0.0868

Gnomad SAS

AF:

0.140

Gnomad FIN

AF:

0.114

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.118

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

GnomAD4 genome

AF:

0.129

AC:

19642

AN:

152072

Hom.:

1457

Cov.:

AF XY:

0.130

AC XY:

9639

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.193

AC:

8016

AN:

41430

American (AMR)

AF:

0.0953

AC:

1456

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.185

AC:

641

AN:

3468

East Asian (EAS)

AF:

0.0868

AC:

450

AN:

5186

South Asian (SAS)

AF:

0.141

AC:

678

AN:

4822

European-Finnish (FIN)

AF:

0.114

AC:

1203

AN:

10570

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.101

AC:

6841

AN:

68002

Other (OTH)

AF:

0.120

AC:

254

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

857

1713

2570

3426

4283

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

208

416

624

832

1040

<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:

0.110

Hom.:

4080

Bravo

AF:

0.128

Asia WGS

AF:

0.141

AC:

488

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.35

(source)

DANN

Benign

0.77

PhyloP100

-0.46

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