dbSNP rs10513442: ENSG00000289885:n.618+21815A>T (chr3-153273601-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000757134.1(ENSG00000289885):n.618+21815A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0384 in 152,302 control chromosomes in the GnomAD database, including 154 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 0.038 ( 154 hom., cov: 32)

Consequence

ENSG00000289885
ENST00000757134.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.918

Publications

1 publications found

Variant links:

Genes affected

ENSG00000289885 (HGNC:):

ENSG00000289885 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=-0.98).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0589 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
ENSG00000289885	ENST00000757134.1 link	n.618+21815A>T		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes

AF:

0.0384

AC:

5841

AN:

152184

Hom.:

154

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0114

Gnomad AMI

AF:

0.108

Gnomad AMR

AF:

0.0365

Gnomad ASJ

AF:

0.0645

Gnomad EAS

AF:

0.00636

Gnomad SAS

AF:

0.0311

Gnomad FIN

AF:

0.00895

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0605

Gnomad OTH

AF:

0.0382

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

GnomAD4 genome

AF:

0.0384

AC:

5841

AN:

152302

Hom.:

154

Cov.:

AF XY:

0.0362

AC XY:

2697

AN XY:

74480

show subpopulations

African (AFR)

AF:

0.0114

AC:

473

AN:

41574

American (AMR)

AF:

0.0365

AC:

558

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0645

AC:

224

AN:

3472

East Asian (EAS)

AF:

0.00638

AC:

AN:

5174

South Asian (SAS)

AF:

0.0321

AC:

155

AN:

4826

European-Finnish (FIN)

AF:

0.00895

AC:

AN:

10618

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0605

AC:

4114

AN:

68012

Other (OTH)

AF:

0.0378

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

306

613

919

1226

1532

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

136

204

272

340

<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:

0.0455

Hom.:

Bravo

AF:

0.0388

Asia WGS

AF:

0.0200

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.68

(source)

DANN

Benign

0.75

PhyloP100

-0.92

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