dbSNP rs1843217: ENSG00000290802:n.232+251A>G (chr2-88824725-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000434790.2(ENSG00000290802):n.232+251A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,102 control chromosomes in the GnomAD database, including 888 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 ( 888 hom., cov: 32)

Consequence

ENSG00000290802
ENST00000434790.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.15

Publications

6 publications found

Variant links:

Genes affected

ENSG00000290802 (HGNC:):

ENSG00000290802 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.142 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
ENSG00000290802	ENST00000434790.2 link	n.232+251A>G		intron_variant	Intron 1 of 2	5
ENSG00000240040	ENST00000624935.3 link	n.40-6296A>G		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15757

AN:

151984

Hom.:

890

Cov.:

show subpopulations

Gnomad AFR

AF:

0.146

Gnomad AMI

AF:

0.0581

Gnomad AMR

AF:

0.0933

Gnomad ASJ

AF:

0.0646

Gnomad EAS

AF:

0.0381

Gnomad SAS

AF:

0.0721

Gnomad FIN

AF:

0.0835

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0945

Gnomad OTH

AF:

0.0799

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

GnomAD4 genome

AF:

0.104

AC:

15775

AN:

152102

Hom.:

888

Cov.:

AF XY:

0.101

AC XY:

7534

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.145

AC:

6031

AN:

41480

American (AMR)

AF:

0.0933

AC:

1426

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.0646

AC:

224

AN:

3468

East Asian (EAS)

AF:

0.0384

AC:

198

AN:

5158

South Asian (SAS)

AF:

0.0722

AC:

347

AN:

4808

European-Finnish (FIN)

AF:

0.0835

AC:

885

AN:

10596

Middle Eastern (MID)

AF:

0.0544

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0945

AC:

6424

AN:

67994

Other (OTH)

AF:

0.0810

AC:

171

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

706

1411

2117

2822

3528

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

178

356

534

712

890

<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:

0.0946

Hom.:

1375

Bravo

AF:

0.107

Asia WGS

AF:

0.0650

AC:

227

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

7.4

(source)

DANN

Benign

0.71

PhyloP100

1.1

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