dbSNP rs17483987: ENSG00000282890:n.302+53673C>T (chr2-48863314-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 ENST00000634588.1(ENSG00000282890):n.302+53673C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,190 control chromosomes in the GnomAD database, including 1,203 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 0.11 ( 1203 hom., cov: 33)

Consequence

ENSG00000282890
ENST00000634588.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.992

Publications

1 publications found

Variant links:

Genes affected

ENSG00000282890 (HGNC:58158):

ENSG00000282890 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.163 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
ENSG00000282890	ENST00000634588.1 link	n.302+53673C>T		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes

AF:

0.111

AC:

16944

AN:

152072

Hom.:

1204

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0378

Gnomad AMI

AF:

0.0789

Gnomad AMR

AF:

0.0950

Gnomad ASJ

AF:

0.174

Gnomad EAS

AF:

0.174

Gnomad SAS

AF:

0.149

Gnomad FIN

AF:

0.197

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.136

Gnomad OTH

AF:

0.116

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

GnomAD4 genome

AF:

0.111

AC:

16933

AN:

152190

Hom.:

1203

Cov.:

AF XY:

0.115

AC XY:

8540

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.0378

AC:

1569

AN:

41554

American (AMR)

AF:

0.0949

AC:

1450

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.174

AC:

604

AN:

3470

East Asian (EAS)

AF:

0.173

AC:

893

AN:

5170

South Asian (SAS)

AF:

0.149

AC:

717

AN:

4824

European-Finnish (FIN)

AF:

0.197

AC:

2085

AN:

10584

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.136

AC:

9269

AN:

67996

Other (OTH)

AF:

0.115

AC:

242

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

789

1577

2366

3154

3943

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

202

404

606

808

1010

<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:

0.114

Hom.:

152

Bravo

AF:

0.102

Asia WGS

AF:

0.127

AC:

441

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.90

(source)

DANN

Benign

0.47

PhyloP100

-0.99

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