dbSNP rs1443010: ENSG00000286605:n.528-2827T>C (chr18-30409800-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000657542.1(ENSG00000286605):n.528-2827T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0323 in 152,292 control chromosomes in the GnomAD database, including 206 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 0.032 ( 206 hom., cov: 32)

Consequence

ENSG00000286605
ENST00000657542.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.530

Publications

3 publications found

Variant links:

Genes affected

ENSG00000286605 (HGNC:):

ENSG00000286605 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 (EAS) allele frequency at 95% confidence interval = 0.115 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
ENSG00000286605	ENST00000657542.1 link	n.528-2827T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0322

AC:

4899

AN:

152174

Hom.:

201

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0459

Gnomad AMI

AF:

0.00989

Gnomad AMR

AF:

0.110

Gnomad ASJ

AF:

0.00893

Gnomad EAS

AF:

0.123

Gnomad SAS

AF:

0.0124

Gnomad FIN

AF:

0.00480

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00667

Gnomad OTH

AF:

0.0316

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

GnomAD4 genome

AF:

0.0323

AC:

4919

AN:

152292

Hom.:

206

Cov.:

AF XY:

0.0341

AC XY:

2540

AN XY:

74466

show subpopulations

African (AFR)

AF:

0.0459

AC:

1910

AN:

41572

American (AMR)

AF:

0.111

AC:

1700

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.00893

AC:

AN:

3470

East Asian (EAS)

AF:

0.123

AC:

635

AN:

5158

South Asian (SAS)

AF:

0.0126

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.00480

AC:

AN:

10620

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00667

AC:

454

AN:

68036

Other (OTH)

AF:

0.0308

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

230

460

691

921

1151

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

192

240

<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:

0.0145

Hom.:

115

Bravo

AF:

0.0416

Asia WGS

AF:

0.0590

AC:

204

AN:

3478

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

0.69

PhyloP100

0.53

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