dbSNP rs2362626: ENSG00000302498:n.219+3308C>G (chr3-190804092-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000787366.1(ENSG00000302498):n.219+3308C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,156 control chromosomes in the GnomAD database, including 2,861 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 0.19 ( 2861 hom., cov: 32)

Consequence

ENSG00000302498
ENST00000787366.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.64

Publications

1 publications found

Variant links:

Genes affected

ENSG00000302498 (HGNC:):

ENSG00000302498 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=-0.94).

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	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302498	ENST00000787366.1 link	n.219+3308C>G		intron_variant	Intron 2 of 3
ENSG00000302498	ENST00000787367.1 link	n.73+3694C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.186

AC:

28212

AN:

152036

Hom.:

2854

Cov.:

show subpopulations

Gnomad AFR

AF:

0.169

Gnomad AMI

AF:

0.0768

Gnomad AMR

AF:

0.202

Gnomad ASJ

AF:

0.154

Gnomad EAS

AF:

0.377

Gnomad SAS

AF:

0.294

Gnomad FIN

AF:

0.272

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.160

Gnomad OTH

AF:

0.180

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

GnomAD4 genome

AF:

0.186

AC:

28249

AN:

152156

Hom.:

2861

Cov.:

AF XY:

0.192

AC XY:

14311

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.169

AC:

7032

AN:

41530

American (AMR)

AF:

0.204

AC:

3109

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.154

AC:

533

AN:

3472

East Asian (EAS)

AF:

0.377

AC:

1948

AN:

5168

South Asian (SAS)

AF:

0.293

AC:

1415

AN:

4822

European-Finnish (FIN)

AF:

0.272

AC:

2873

AN:

10580

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.160

AC:

10850

AN:

67998

Other (OTH)

AF:

0.181

AC:

382

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1160

2319

3479

4638

5798

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

312

624

936

1248

1560

<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:

0.172

Hom.:

311

Bravo

AF:

0.178

Asia WGS

AF:

0.353

AC:

1227

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.17

(source)

DANN

Benign

0.59

PhyloP100

-1.6

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