dbSNP rs6755560: ENSG00000229321:n.347+9847T>C (chr2-206853059-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 ENST00000438070.3(ENSG00000229321):n.347+9847T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 151,686 control chromosomes in the GnomAD database, including 5,559 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 0.26 ( 5559 hom., cov: 31)

Consequence

ENSG00000229321
ENST00000438070.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.583

Publications

7 publications found

Variant links:

Genes affected

ENSG00000229321 (HGNC:):

ENSG00000229321 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 (NFE) allele frequency at 95% confidence interval = 0.311 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
ENSG00000229321	ENST00000438070.3 link	n.347+9847T>C	intron_variant	Intron 2 of 6	3
ENSG00000229321	ENST00000658291.1 link	n.3035-10337T>C	intron_variant	Intron 2 of 3
ENSG00000229321	ENST00000658889.1 link	n.2974-26324T>C	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.262

AC:

39639

AN:

151568

Hom.:

5555

Cov.:

show subpopulations

Gnomad AFR

AF:

0.188

Gnomad AMI

AF:

0.298

Gnomad AMR

AF:

0.303

Gnomad ASJ

AF:

0.322

Gnomad EAS

AF:

0.0297

Gnomad SAS

AF:

0.191

Gnomad FIN

AF:

0.272

Gnomad MID

AF:

0.261

Gnomad NFE

AF:

0.314

Gnomad OTH

AF:

0.268

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

GnomAD4 genome

AF:

0.261

AC:

39656

AN:

151686

Hom.:

5559

Cov.:

AF XY:

0.259

AC XY:

19202

AN XY:

74102

show subpopulations

African (AFR)

AF:

0.188

AC:

7761

AN:

41342

American (AMR)

AF:

0.304

AC:

4632

AN:

15248

Ashkenazi Jewish (ASJ)

AF:

0.322

AC:

1115

AN:

3468

East Asian (EAS)

AF:

0.0295

AC:

152

AN:

5146

South Asian (SAS)

AF:

0.191

AC:

910

AN:

4774

European-Finnish (FIN)

AF:

0.272

AC:

2859

AN:

10522

Middle Eastern (MID)

AF:

0.253

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.314

AC:

21323

AN:

67880

Other (OTH)

AF:

0.266

AC:

559

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1457

2915

4372

5830

7287

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

404

808

1212

1616

2020

<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:

0.283

Hom.:

11046

Bravo

AF:

0.258

Asia WGS

AF:

0.120

AC:

420

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

4.5

(source)

DANN

Benign

0.69

PhyloP100

-0.58

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