dbSNP rs2505989: ENSG00000303432:n.257+3303C>G (chr10-43068003-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 ENST00000794440.1(ENSG00000303432):n.257+3303C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,158 control chromosomes in the GnomAD database, including 8,753 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 0.33 ( 8753 hom., cov: 33)

Consequence

ENSG00000303432
ENST00000794440.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.320

Publications

0 publications found

Variant links:

Genes affected

ENSG00000303432 (HGNC:):

ENSG00000303432 links:

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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 (NFE) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000303432	ENST00000794440.1 link	n.257+3303C>G	intron_variant	Intron 2 of 2
ENSG00000303432	ENST00000794441.1 link	n.323-152C>G	intron_variant	Intron 2 of 3
ENSG00000303432	ENST00000794442.1 link	n.314-118C>G	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.326

AC:

49596

AN:

152040

Hom.:

8746

Cov.:

show subpopulations

Gnomad AFR

AF:

0.233

Gnomad AMI

AF:

0.468

Gnomad AMR

AF:

0.343

Gnomad ASJ

AF:

0.307

Gnomad EAS

AF:

0.0811

Gnomad SAS

AF:

0.324

Gnomad FIN

AF:

0.397

Gnomad MID

AF:

0.332

Gnomad NFE

AF:

0.387

Gnomad OTH

AF:

0.297

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

GnomAD4 genome

AF:

0.326

AC:

49618

AN:

152158

Hom.:

8753

Cov.:

AF XY:

0.325

AC XY:

24155

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.233

AC:

9681

AN:

41528

American (AMR)

AF:

0.343

AC:

5249

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.307

AC:

1065

AN:

3470

East Asian (EAS)

AF:

0.0811

AC:

420

AN:

5176

South Asian (SAS)

AF:

0.324

AC:

1561

AN:

4824

European-Finnish (FIN)

AF:

0.397

AC:

4196

AN:

10568

Middle Eastern (MID)

AF:

0.337

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.387

AC:

26299

AN:

67978

Other (OTH)

AF:

0.295

AC:

622

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1701

3401

5102

6802

8503

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

482

964

1446

1928

2410

<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:

0.351

Hom.:

1210

Bravo

AF:

0.319

Asia WGS

AF:

0.204

AC:

712

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

2.7

(source)

DANN

Benign

0.43

PhyloP100

-0.32

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