dbSNP rs7020422: ENSG00000286536:n.1857+52675C>T (chr9-105114945-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 ENST00000666856.1(ENSG00000286536):n.1857+52675C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 152,172 control chromosomes in the GnomAD database, including 6,902 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 0.27 ( 6902 hom., cov: 33)

Consequence

ENSG00000286536
ENST00000666856.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.842

Publications

4 publications found

Variant links:

Genes affected

ENSG00000286536 (HGNC:):

ENSG00000286536 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376197	XR_930205.3 link	n.177-3786G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286536	ENST00000666856.1 link	n.1857+52675C>T		intron_variant	Intron 7 of 7

Frequencies

GnomAD3 genomes

AF:

0.266

AC:

40484

AN:

152054

Hom.:

6875

Cov.:

show subpopulations

Gnomad AFR

AF:

0.486

Gnomad AMI

AF:

0.174

Gnomad AMR

AF:

0.179

Gnomad ASJ

AF:

0.155

Gnomad EAS

AF:

0.302

Gnomad SAS

AF:

0.188

Gnomad FIN

AF:

0.153

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.181

Gnomad OTH

AF:

0.244

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

GnomAD4 genome

AF:

0.267

AC:

40557

AN:

152172

Hom.:

6902

Cov.:

AF XY:

0.263

AC XY:

19540

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.486

AC:

20169

AN:

41506

American (AMR)

AF:

0.179

AC:

2730

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.155

AC:

535

AN:

3460

East Asian (EAS)

AF:

0.303

AC:

1568

AN:

5172

South Asian (SAS)

AF:

0.189

AC:

909

AN:

4820

European-Finnish (FIN)

AF:

0.153

AC:

1623

AN:

10596

Middle Eastern (MID)

AF:

0.248

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.181

AC:

12280

AN:

68004

Other (OTH)

AF:

0.242

AC:

512

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1431

2863

4294

5726

7157

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

392

784

1176

1568

1960

<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:

0.222

Hom.:

809

Bravo

AF:

0.281

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

4.6

(source)

DANN

Benign

0.61

PhyloP100

0.84

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