dbSNP rs9289146: ENSG00000286735:n.169+17903C>T (chr3-120517482-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000732215.1(ENSG00000286735):n.169+17903C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,174 control chromosomes in the GnomAD database, including 2,161 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 ( 2161 hom., cov: 32)

Consequence

ENSG00000286735
ENST00000732215.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.200

Publications

6 publications found

Variant links:

Genes affected

ENSG00000286735 (HGNC:):

ENSG00000286735 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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286735	ENST00000732215.1 link	n.169+17903C>T	intron_variant	Intron 2 of 3
ENSG00000286735	ENST00000732216.1 link	n.246+17903C>T	intron_variant	Intron 2 of 2
ENSG00000295741	ENST00000732308.1 link	n.127+43324G>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.164

AC:

24893

AN:

152056

Hom.:

2154

Cov.:

show subpopulations

Gnomad AFR

AF:

0.181

Gnomad AMI

AF:

0.129

Gnomad AMR

AF:

0.128

Gnomad ASJ

AF:

0.238

Gnomad EAS

AF:

0.0396

Gnomad SAS

AF:

0.114

Gnomad FIN

AF:

0.184

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.167

Gnomad OTH

AF:

0.177

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

GnomAD4 genome

AF:

0.164

AC:

24924

AN:

152174

Hom.:

2161

Cov.:

AF XY:

0.163

AC XY:

12163

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.181

AC:

7518

AN:

41512

American (AMR)

AF:

0.128

AC:

1960

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.238

AC:

827

AN:

3470

East Asian (EAS)

AF:

0.0397

AC:

206

AN:

5186

South Asian (SAS)

AF:

0.113

AC:

544

AN:

4812

European-Finnish (FIN)

AF:

0.184

AC:

1954

AN:

10606

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.167

AC:

11366

AN:

67976

Other (OTH)

AF:

0.175

AC:

371

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1075

2150

3225

4300

5375

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

272

544

816

1088

1360

<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:

0.165

Hom.:

4723

Bravo

AF:

0.159

Asia WGS

AF:

0.115

AC:

400

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

7.5

(source)

DANN

Benign

0.20

PhyloP100

0.20

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