dbSNP rs8043884: ENSG00000259846:n.439+14287C>A (chr16-64549363-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000564046.1(ENSG00000259846):n.439+14287C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 151,976 control chromosomes in the GnomAD database, including 4,244 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 0.23 ( 4244 hom., cov: 32)

Consequence

ENSG00000259846
ENST00000564046.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.13

Publications

4 publications found

Variant links:

Genes affected

ENSG00000259846 (HGNC:):

ENSG00000259846 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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000259846	ENST00000564046.1 link	n.439+14287C>A	intron_variant	Intron 4 of 4	4
ENSG00000259846	ENST00000808892.1 link	n.418-50776C>A	intron_variant	Intron 3 of 4
ENSG00000259846	ENST00000808893.1 link	n.404-50776C>A	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.230

AC:

34994

AN:

151858

Hom.:

4244

Cov.:

show subpopulations

Gnomad AFR

AF:

0.188

Gnomad AMI

AF:

0.336

Gnomad AMR

AF:

0.202

Gnomad ASJ

AF:

0.270

Gnomad EAS

AF:

0.00581

Gnomad SAS

AF:

0.237

Gnomad FIN

AF:

0.256

Gnomad MID

AF:

0.223

Gnomad NFE

AF:

0.272

Gnomad OTH

AF:

0.222

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

GnomAD4 genome

AF:

0.230

AC:

35003

AN:

151976

Hom.:

4244

Cov.:

AF XY:

0.228

AC XY:

16932

AN XY:

74284

show subpopulations

African (AFR)

AF:

0.188

AC:

7778

AN:

41450

American (AMR)

AF:

0.202

AC:

3082

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.270

AC:

938

AN:

3470

East Asian (EAS)

AF:

0.00601

AC:

AN:

5154

South Asian (SAS)

AF:

0.238

AC:

1144

AN:

4814

European-Finnish (FIN)

AF:

0.256

AC:

2699

AN:

10540

Middle Eastern (MID)

AF:

0.219

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.272

AC:

18498

AN:

67984

Other (OTH)

AF:

0.220

AC:

463

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1365

2730

4096

5461

6826

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

378

756

1134

1512

1890

<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:

0.155

Hom.:

363

Bravo

AF:

0.224

Asia WGS

AF:

0.126

AC:

440

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.092

(source)

DANN

Benign

0.46

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