dbSNP rs2189555: ENSG00000230333:n.113+36149C>T (chr7-11289374-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 ENST00000421121.5(ENSG00000230333):n.113+36149C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 151,878 control chromosomes in the GnomAD database, including 1,065 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 0.10 ( 1065 hom., cov: 32)

Consequence

ENSG00000230333
ENST00000421121.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0160

Publications

2 publications found

Variant links:

Genes affected

ENSG00000230333 (HGNC:):

ENSG00000230333 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=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000230333	ENST00000421121.5 link	n.113+36149C>T	intron_variant	Intron 1 of 2	1
ENSG00000230333	ENST00000428533.5 link	n.139-89913C>T	intron_variant	Intron 1 of 2	5
ENSG00000230333	ENST00000428967.5 link	n.497+40999C>T	intron_variant	Intron 4 of 4	4

Frequencies

GnomAD3 genomes

AF:

0.102

AC:

15435

AN:

151758

Hom.:

1066

Cov.:

show subpopulations

Gnomad AFR

AF:

0.101

Gnomad AMI

AF:

0.0526

Gnomad AMR

AF:

0.145

Gnomad ASJ

AF:

0.0704

Gnomad EAS

AF:

0.377

Gnomad SAS

AF:

0.123

Gnomad FIN

AF:

0.131

Gnomad MID

AF:

0.0924

Gnomad NFE

AF:

0.0678

Gnomad OTH

AF:

0.0983

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

GnomAD4 genome

AF:

0.102

AC:

15457

AN:

151878

Hom.:

1065

Cov.:

AF XY:

0.107

AC XY:

7946

AN XY:

74212

show subpopulations

African (AFR)

AF:

0.102

AC:

4225

AN:

41482

American (AMR)

AF:

0.145

AC:

2205

AN:

15230

Ashkenazi Jewish (ASJ)

AF:

0.0704

AC:

244

AN:

3466

East Asian (EAS)

AF:

0.377

AC:

1921

AN:

5098

South Asian (SAS)

AF:

0.122

AC:

588

AN:

4808

European-Finnish (FIN)

AF:

0.131

AC:

1384

AN:

10586

Middle Eastern (MID)

AF:

0.0993

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0678

AC:

4606

AN:

67896

Other (OTH)

AF:

0.0982

AC:

207

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

664

1327

1991

2654

3318

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

174

348

522

696

870

<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:

0.0933

Hom.:

116

Bravo

AF:

0.105

Asia WGS

AF:

0.213

AC:

738

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

8.3

(source)

DANN

Benign

0.78

PhyloP100

0.016

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