dbSNP rs17043388: ENSG00000229642:n.291+22530T>A (chr3-5719016-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000425894.2(ENSG00000229642):n.291+22530T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0841 in 152,122 control chromosomes in the GnomAD database, including 895 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 0.084 ( 895 hom., cov: 32)

Consequence

ENSG00000229642
ENST00000425894.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.494

Publications

1 publications found

Variant links:

Genes affected

ENSG00000229642 (HGNC:):

ENSG00000229642 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 = 0.187 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
ENSG00000229642	ENST00000425894.2 link	n.291+22530T>A	intron_variant	Intron 2 of 8	3
ENSG00000229642	ENST00000779001.1 link	n.212+22530T>A	intron_variant	Intron 2 of 7
ENSG00000229642	ENST00000779002.1 link	n.232+22530T>A	intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes

AF:

0.0839

AC:

12755

AN:

152004

Hom.:

886

Cov.:

show subpopulations

Gnomad AFR

AF:

0.190

Gnomad AMI

AF:

0.0987

Gnomad AMR

AF:

0.0576

Gnomad ASJ

AF:

0.0571

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0236

Gnomad FIN

AF:

0.0372

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.0442

Gnomad OTH

AF:

0.0823

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

GnomAD4 genome

AF:

0.0841

AC:

12791

AN:

152122

Hom.:

895

Cov.:

AF XY:

0.0820

AC XY:

6098

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.191

AC:

7903

AN:

41474

American (AMR)

AF:

0.0575

AC:

879

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0571

AC:

198

AN:

3470

East Asian (EAS)

AF:

0.000580

AC:

AN:

5176

South Asian (SAS)

AF:

0.0234

AC:

113

AN:

4820

European-Finnish (FIN)

AF:

0.0372

AC:

394

AN:

10594

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0442

AC:

3005

AN:

67996

Other (OTH)

AF:

0.0819

AC:

173

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

562

1124

1685

2247

2809

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

136

272

408

544

680

<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:

0.0688

Hom.:

Bravo

AF:

0.0898

Asia WGS

AF:

0.0260

AC:

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

0.15

(source)

DANN

Benign

0.70

PhyloP100

-0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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