dbSNP rs9568856: ENSG00000287722:n.629+186724G>A (chr13-53490846-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000657016.1(ENSG00000287722):n.629+186724G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 151,818 control chromosomes in the GnomAD database, including 4,421 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 0.22 ( 4421 hom., cov: 32)

Consequence

ENSG00000287722
ENST00000657016.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.271

Publications

40 publications found

Variant links:

Genes affected

ENSG00000287722 (HGNC:):

ENSG00000287722 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.37).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000287722	ENST00000657016.1 link	n.629+186724G>A	intron_variant	Intron 2 of 3
ENSG00000288768	ENST00000748644.1 link	n.714+20556G>A	intron_variant	Intron 5 of 6
ENSG00000288768	ENST00000748645.1 link	n.564+20556G>A	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.218

AC:

33009

AN:

151698

Hom.:

4409

Cov.:

show subpopulations

Gnomad AFR

AF:

0.346

Gnomad AMI

AF:

0.269

Gnomad AMR

AF:

0.312

Gnomad ASJ

AF:

0.174

Gnomad EAS

AF:

0.297

Gnomad SAS

AF:

0.229

Gnomad FIN

AF:

0.124

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.129

Gnomad OTH

AF:

0.188

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

GnomAD4 genome

AF:

0.218

AC:

33066

AN:

151818

Hom.:

4421

Cov.:

AF XY:

0.220

AC XY:

16321

AN XY:

74246

show subpopulations

African (AFR)

AF:

0.346

AC:

14321

AN:

41400

American (AMR)

AF:

0.312

AC:

4745

AN:

15202

Ashkenazi Jewish (ASJ)

AF:

0.174

AC:

602

AN:

3464

East Asian (EAS)

AF:

0.297

AC:

1533

AN:

5156

South Asian (SAS)

AF:

0.229

AC:

1104

AN:

4820

European-Finnish (FIN)

AF:

0.124

AC:

1316

AN:

10596

Middle Eastern (MID)

AF:

0.170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.129

AC:

8746

AN:

67870

Other (OTH)

AF:

0.192

AC:

404

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1254

2509

3763

5018

6272

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

346

692

1038

1384

1730

<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:

0.158

Hom.:

9875

Bravo

AF:

0.240

Asia WGS

AF:

0.266

AC:

924

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.37

CADD

Benign

(source)

DANN

Benign

0.86

PhyloP100

-0.27

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