dbSNP rs2698541: ENSG00000288932:n.779+1196G>A (chr2-64261545-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000717282.1(ENSG00000288932):n.779+1196G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 151,966 control chromosomes in the GnomAD database, including 6,783 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 0.29 ( 6783 hom., cov: 32)

Consequence

ENSG00000288932
ENST00000717282.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.596

Publications

5 publications found

Variant links:

Genes affected

ENSG00000288932 (HGNC:):

ENSG00000288932 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=-0.75).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000288932	ENST00000717282.1 link	n.779+1196G>A	intron_variant	Intron 5 of 5
ENSG00000288932	ENST00000717283.1 link	n.254+31905G>A	intron_variant	Intron 2 of 3
ENSG00000288932	ENST00000717284.1 link	n.211-29600G>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.291

AC:

44153

AN:

151846

Hom.:

6772

Cov.:

show subpopulations

Gnomad AFR

AF:

0.245

Gnomad AMI

AF:

0.210

Gnomad AMR

AF:

0.331

Gnomad ASJ

AF:

0.298

Gnomad EAS

AF:

0.632

Gnomad SAS

AF:

0.436

Gnomad FIN

AF:

0.271

Gnomad MID

AF:

0.277

Gnomad NFE

AF:

0.277

Gnomad OTH

AF:

0.288

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

GnomAD4 genome

AF:

0.291

AC:

44197

AN:

151966

Hom.:

6783

Cov.:

AF XY:

0.293

AC XY:

21736

AN XY:

74266

show subpopulations

African (AFR)

AF:

0.245

AC:

10137

AN:

41422

American (AMR)

AF:

0.331

AC:

5056

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.298

AC:

1033

AN:

3470

East Asian (EAS)

AF:

0.632

AC:

3270

AN:

5172

South Asian (SAS)

AF:

0.435

AC:

2095

AN:

4816

European-Finnish (FIN)

AF:

0.271

AC:

2862

AN:

10542

Middle Eastern (MID)

AF:

0.293

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.277

AC:

18841

AN:

67954

Other (OTH)

AF:

0.297

AC:

627

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1582

3165

4747

6330

7912

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

450

900

1350

1800

2250

<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:

0.280

Hom.:

8144

Bravo

AF:

0.294

Asia WGS

AF:

0.535

AC:

1855

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

1.7

(source)

DANN

Benign

0.75

PhyloP100

-0.60

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