dbSNP rs1009748: ENSG00000282478:n.453-251G>A (chr20-11410118-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000784484.1(ENSG00000282478):n.453-251G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 151,874 control chromosomes in the GnomAD database, including 7,100 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 ( 7100 hom., cov: 32)

Consequence

ENSG00000282478
ENST00000784484.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0200

Publications

2 publications found

Variant links:

Genes affected

ENSG00000282478 (HGNC:):

ENSG00000282478 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 = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372529	XR_937261.2 link	n.57+17120G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000282478	ENST00000784484.1 link	n.453-251G>A		intron_variant	Intron 2 of 2
ENSG00000302131	ENST00000784589.1 link	n.75+17120G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.287

AC:

43495

AN:

151754

Hom.:

7093

Cov.:

show subpopulations

Gnomad AFR

AF:

0.123

Gnomad AMI

AF:

0.277

Gnomad AMR

AF:

0.310

Gnomad ASJ

AF:

0.262

Gnomad EAS

AF:

0.471

Gnomad SAS

AF:

0.381

Gnomad FIN

AF:

0.304

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.358

Gnomad OTH

AF:

0.312

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

GnomAD4 genome

AF:

0.287

AC:

43514

AN:

151874

Hom.:

7100

Cov.:

AF XY:

0.286

AC XY:

21194

AN XY:

74192

show subpopulations

African (AFR)

AF:

0.123

AC:

5093

AN:

41468

American (AMR)

AF:

0.310

AC:

4733

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.262

AC:

907

AN:

3464

East Asian (EAS)

AF:

0.471

AC:

2429

AN:

5156

South Asian (SAS)

AF:

0.379

AC:

1819

AN:

4802

European-Finnish (FIN)

AF:

0.304

AC:

3192

AN:

10490

Middle Eastern (MID)

AF:

0.269

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.358

AC:

24345

AN:

67934

Other (OTH)

AF:

0.316

AC:

665

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1492

2984

4476

5968

7460

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

462

924

1386

1848

2310

<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:

0.345

Hom.:

14492

Bravo

AF:

0.282

Asia WGS

AF:

0.408

AC:

1411

AN:

3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.4

(source)

DANN

Benign

0.48

PhyloP100

0.020

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