Genetic Variant SLC1A2-AS1:n.426+3197A>G (chr11-35241591-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000844195.1(SLC1A2-AS1):n.426+3197A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 152,180 control chromosomes in the GnomAD database, including 49,675 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 0.80 ( 49675 hom., cov: 32)

Consequence

SLC1A2-AS1
ENST00000844195.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.02

Publications

2 publications found

Variant links:

Genes affected

SLC1A2-AS1 (HGNC:40534): (SLC1A2 antisense RNA 1)

SLC1A2-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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
SLC1A2-AS1	ENST00000844195.1 link	n.426+3197A>G	intron_variant	Intron 1 of 2
SLC1A2-AS1	ENST00000844196.1 link	n.328+3197A>G	intron_variant	Intron 1 of 1
SLC1A2-AS1	ENST00000844197.1 link	n.425+3197A>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.801

AC:

121759

AN:

152062

Hom.:

49615

Cov.:

show subpopulations

Gnomad AFR

AF:

0.944

Gnomad AMI

AF:

0.721

Gnomad AMR

AF:

0.823

Gnomad ASJ

AF:

0.817

Gnomad EAS

AF:

0.928

Gnomad SAS

AF:

0.782

Gnomad FIN

AF:

0.717

Gnomad MID

AF:

0.851

Gnomad NFE

AF:

0.713

Gnomad OTH

AF:

0.797

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

GnomAD4 genome

AF:

0.801

AC:

121882

AN:

152180

Hom.:

49675

Cov.:

AF XY:

0.805

AC XY:

59853

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.944

AC:

39219

AN:

41558

American (AMR)

AF:

0.823

AC:

12585

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.817

AC:

2836

AN:

3472

East Asian (EAS)

AF:

0.928

AC:

4795

AN:

5166

South Asian (SAS)

AF:

0.783

AC:

3778

AN:

4828

European-Finnish (FIN)

AF:

0.717

AC:

7575

AN:

10558

Middle Eastern (MID)

AF:

0.857

AC:

252

AN:

294

European-Non Finnish (NFE)

AF:

0.713

AC:

48495

AN:

67982

Other (OTH)

AF:

0.800

AC:

1689

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1209

2419

3628

4838

6047

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

860

1720

2580

3440

4300

<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:

0.707

Hom.:

3402

Bravo

AF:

0.816

Asia WGS

AF:

0.855

AC:

2969

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.043

(source)

DANN

Benign

0.51

PhyloP100

-1.0

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