dbSNP rs2243737: ENSG00000286250:n.77+1173A>T (chr20-52893967-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000652426.2(ENSG00000286250):n.77+1173A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 151,940 control chromosomes in the GnomAD database, including 10,536 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 0.37 ( 10536 hom., cov: 32)

Consequence

ENSG00000286250
ENST00000652426.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.418

Publications

2 publications found

Variant links:

Genes affected

ENSG00000286250 (HGNC:):

ENSG00000286250 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 (SAS) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372668	XR_936864.3 link	n.287+1173A>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286250	ENST00000652426.2 link	n.77+1173A>T	intron_variant	Intron 1 of 3
ENSG00000304154	ENST00000800119.1 link	n.151-2604T>A	intron_variant	Intron 1 of 2
ENSG00000304154	ENST00000800120.1 link	n.162-1451T>A	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.368

AC:

55933

AN:

151822

Hom.:

10532

Cov.:

show subpopulations

Gnomad AFR

AF:

0.340

Gnomad AMI

AF:

0.322

Gnomad AMR

AF:

0.375

Gnomad ASJ

AF:

0.380

Gnomad EAS

AF:

0.493

Gnomad SAS

AF:

0.571

Gnomad FIN

AF:

0.415

Gnomad MID

AF:

0.415

Gnomad NFE

AF:

0.353

Gnomad OTH

AF:

0.366

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

GnomAD4 genome

AF:

0.368

AC:

55954

AN:

151940

Hom.:

10536

Cov.:

AF XY:

0.379

AC XY:

28113

AN XY:

74238

show subpopulations

African (AFR)

AF:

0.339

AC:

14066

AN:

41454

American (AMR)

AF:

0.375

AC:

5716

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.380

AC:

1320

AN:

3472

East Asian (EAS)

AF:

0.493

AC:

2544

AN:

5156

South Asian (SAS)

AF:

0.571

AC:

2748

AN:

4810

European-Finnish (FIN)

AF:

0.415

AC:

4373

AN:

10548

Middle Eastern (MID)

AF:

0.408

AC:

120

AN:

294

European-Non Finnish (NFE)

AF:

0.353

AC:

23997

AN:

67936

Other (OTH)

AF:

0.368

AC:

778

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1806

3612

5419

7225

9031

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

564

1128

1692

2256

2820

<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:

0.355

Hom.:

1186

Bravo

AF:

0.362

Asia WGS

AF:

0.506

AC:

1754

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.0

(source)

DANN

Benign

0.41

PhyloP100

0.42

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