dbSNP rs2301252: ENSG00000273677:n.71C>A (chr11-32436381-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000613208.1(ENSG00000273677):n.71C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 152,242 control chromosomes in the GnomAD database, including 19,683 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 0.48 ( 19652 hom., cov: 33)

Exomes 𝑓: 0.52 ( 31 hom. )

Consequence

ENSG00000273677
ENST00000613208.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.116

Publications

5 publications found

Variant links:

Genes affected

ENSG00000273677 (HGNC:):

ENSG00000273677 links:

WT1-AS (HGNC:18135): (WT1 antisense RNA) This gene is located upstream of the Wilms tumor 1 (WT1) gene; these two genes are bi-directionally transcribed from the same promoter region. This gene is imprinted in kidney, with preferential expression from the paternal allele. Imprinting defects at chromosome 11p13 may contribute to tumorigenesis. [provided by RefSeq, May 2014]

WT1-AS 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=-0.73).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
WT1-AS	NR_120546.1 link	n.343C>A	non_coding_transcript_exon_variant	Exon 1 of 2
WT1-AS	NR_023920.2 link	n.329+535C>A	intron_variant	Intron 1 of 1
WT1-AS	NR_120547.1 link	n.329+535C>A	intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000273677	ENST00000613208.1 link	n.71C>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
WT1-AS	ENST00000686872.2 link	n.756C>A	non_coding_transcript_exon_variant	Exon 1 of 1
WT1-AS	ENST00000395900.1 link	n.268+535C>A	intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes

AF:

0.484

AC:

73485

AN:

151886

Hom.:

19603

Cov.:

show subpopulations

Gnomad AFR

AF:

0.684

Gnomad AMI

AF:

0.294

Gnomad AMR

AF:

0.493

Gnomad ASJ

AF:

0.397

Gnomad EAS

AF:

0.754

Gnomad SAS

AF:

0.642

Gnomad FIN

AF:

0.319

Gnomad MID

AF:

0.563

Gnomad NFE

AF:

0.360

Gnomad OTH

AF:

0.502

GnomAD4 exome

AF:

0.517

AC:

123

AN:

238

Hom.:

Cov.:

AF XY:

0.512

AC XY:

AN XY:

166

show subpopulations

African (AFR)

AF:

0.667

AC:

AN:

American (AMR)

AF:

0.750

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.750

AC:

AN:

South Asian (SAS)

AF:

0.700

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.490

AC:

AN:

198

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.537

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.484

AC:

73587

AN:

152004

Hom.:

19652

Cov.:

AF XY:

0.488

AC XY:

36261

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.684

AC:

28361

AN:

41476

American (AMR)

AF:

0.494

AC:

7544

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.397

AC:

1377

AN:

3470

East Asian (EAS)

AF:

0.754

AC:

3858

AN:

5120

South Asian (SAS)

AF:

0.643

AC:

3096

AN:

4818

European-Finnish (FIN)

AF:

0.319

AC:

3365

AN:

10552

Middle Eastern (MID)

AF:

0.554

AC:

163

AN:

294

European-Non Finnish (NFE)

AF:

0.360

AC:

24479

AN:

67970

Other (OTH)

AF:

0.509

AC:

1076

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1798

3597

5395

7194

8992

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

648

1296

1944

2592

3240

<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:

0.363

Hom.:

1473

Bravo

AF:

0.502

Asia WGS

AF:

0.710

AC:

2471

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

5.4

(source)

DANN

Benign

0.76

PhyloP100

-0.12

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over