dbSNP rs17007761: ENSG00000286481:n.756-64804C>A (chr2-122468047-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 ENST00000657880.2(ENSG00000286481):n.756-64804C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0621 in 152,192 control chromosomes in the GnomAD database, including 451 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 0.062 ( 451 hom., cov: 32)

Consequence

ENSG00000286481
ENST00000657880.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.283

Publications

5 publications found

Variant links:

Genes affected

ENSG00000286481 (HGNC:):

ENSG00000286481 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=-0.87).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286481	ENST00000657880.2 link	n.756-64804C>A	intron_variant	Intron 3 of 8
ENSG00000287871	ENST00000804613.1 link	n.165-1013G>T	intron_variant	Intron 1 of 1
ENSG00000304587	ENST00000804814.1 link	n.324+1270C>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0621

AC:

9447

AN:

152072

Hom.:

450

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0349

Gnomad AMI

AF:

0.121

Gnomad AMR

AF:

0.155

Gnomad ASJ

AF:

0.0320

Gnomad EAS

AF:

0.102

Gnomad SAS

AF:

0.160

Gnomad FIN

AF:

0.0396

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0521

Gnomad OTH

AF:

0.0661

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

GnomAD4 genome

AF:

0.0621

AC:

9453

AN:

152192

Hom.:

451

Cov.:

AF XY:

0.0654

AC XY:

4865

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.0349

AC:

1451

AN:

41526

American (AMR)

AF:

0.155

AC:

2371

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0320

AC:

111

AN:

3472

East Asian (EAS)

AF:

0.101

AC:

523

AN:

5168

South Asian (SAS)

AF:

0.160

AC:

771

AN:

4820

European-Finnish (FIN)

AF:

0.0396

AC:

419

AN:

10594

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0521

AC:

3541

AN:

68008

Other (OTH)

AF:

0.0687

AC:

145

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

441

882

1323

1764

2205

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

232

348

464

580

<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:

0.0581

Hom.:

1467

Bravo

AF:

0.0693

Asia WGS

AF:

0.176

AC:

610

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.1

(source)

DANN

Benign

0.65

PhyloP100

-0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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