Genetic Variant SLC2A9-AS1:n.384+4778G>A (chr4-10060702-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000733256.1(SLC2A9-AS1):n.384+4778G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 152,150 control chromosomes in the GnomAD database, including 42,060 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 0.74 ( 42060 hom., cov: 34)

Consequence

SLC2A9-AS1
ENST00000733256.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.609

Publications

23 publications found

Variant links:

Genes affected

SLC2A9-AS1 (HGNC:40636): (SLC2A9 antisense RNA 1)

SLC2A9-AS1 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=-0.98).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
SLC2A9-AS1	ENST00000733256.1 link	n.384+4778G>A	intron_variant	Intron 3 of 3
SLC2A9-AS1	ENST00000733257.1 link	n.453+4778G>A	intron_variant	Intron 3 of 3
SLC2A9-AS1	ENST00000733258.1 link	n.255+4778G>A	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.740

AC:

112473

AN:

152032

Hom.:

42035

Cov.:

show subpopulations

Gnomad AFR

AF:

0.753

Gnomad AMI

AF:

0.652

Gnomad AMR

AF:

0.602

Gnomad ASJ

AF:

0.702

Gnomad EAS

AF:

0.524

Gnomad SAS

AF:

0.663

Gnomad FIN

AF:

0.772

Gnomad MID

AF:

0.669

Gnomad NFE

AF:

0.783

Gnomad OTH

AF:

0.740

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

GnomAD4 genome

AF:

0.740

AC:

112537

AN:

152150

Hom.:

42060

Cov.:

AF XY:

0.734

AC XY:

54590

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.753

AC:

31234

AN:

41494

American (AMR)

AF:

0.602

AC:

9194

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.702

AC:

2437

AN:

3472

East Asian (EAS)

AF:

0.525

AC:

2719

AN:

5178

South Asian (SAS)

AF:

0.662

AC:

3186

AN:

4812

European-Finnish (FIN)

AF:

0.772

AC:

8159

AN:

10570

Middle Eastern (MID)

AF:

0.664

AC:

194

AN:

292

European-Non Finnish (NFE)

AF:

0.783

AC:

53264

AN:

68026

Other (OTH)

AF:

0.737

AC:

1557

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1486

2972

4458

5944

7430

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

844

1688

2532

3376

4220

<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:

0.764

Hom.:

125087

Bravo

AF:

0.727

Asia WGS

AF:

0.635

AC:

2213

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.35

(source)

DANN

Benign

0.36

PhyloP100

-0.61

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