dbSNP rs1002229: ENSG00000285283:c.102-65683A>T (chr11-32031461-A-T) – ACMG Classification: Benign (-10 pts)

Variant summary

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

The ENST00000532942.5(ENSG00000285283):c.102-65683A>T variant causes a intron change. The variant allele was found at a frequency of 0.178 in 152,124 control chromosomes in the GnomAD database, including 3,167 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 0.18 ( 3167 hom., cov: 32)

Consequence

ENSG00000285283
ENST00000532942.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.94

Publications

3 publications found

Variant links:

Genes affected

ENSG00000285283 (HGNC:):

ENSG00000285283 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=-0.3).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285283	ENST00000532942.5 link	c.102-65683A>T		intron_variant	Intron 1 of 5	2		ENSP00000436422.1
ENSG00000285283	ENST00000530348.5 link	c.-244-65683A>T		intron_variant	Intron 1 of 3	4		ENSP00000436482.1		E9PP27

Frequencies

GnomAD3 genomes

AF:

0.178

AC:

27001

AN:

152006

Hom.:

3150

Cov.:

show subpopulations

Gnomad AFR

AF:

0.281

Gnomad AMI

AF:

0.114

Gnomad AMR

AF:

0.278

Gnomad ASJ

AF:

0.127

Gnomad EAS

AF:

0.327

Gnomad SAS

AF:

0.296

Gnomad FIN

AF:

0.0711

Gnomad MID

AF:

0.178

Gnomad NFE

AF:

0.0925

Gnomad OTH

AF:

0.179

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

GnomAD4 genome

AF:

0.178

AC:

27069

AN:

152124

Hom.:

3167

Cov.:

AF XY:

0.181

AC XY:

13446

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.282

AC:

11681

AN:

41488

American (AMR)

AF:

0.278

AC:

4253

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.127

AC:

439

AN:

3470

East Asian (EAS)

AF:

0.327

AC:

1690

AN:

5168

South Asian (SAS)

AF:

0.296

AC:

1429

AN:

4824

European-Finnish (FIN)

AF:

0.0711

AC:

753

AN:

10598

Middle Eastern (MID)

AF:

0.178

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0925

AC:

6289

AN:

67988

Other (OTH)

AF:

0.179

AC:

379

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1048

2097

3145

4194

5242

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

276

552

828

1104

1380

<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:

0.132

Hom.:

249

Bravo

AF:

0.201

Asia WGS

AF:

0.273

AC:

948

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.30

CADD

Benign

(source)

DANN

Benign

0.88

PhyloP100

4.9

Mutation Taster

=100/0

polymorphism (auto)

(source)

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