Genetic Variant SNAI3-AS1:n.2007G>C (chr16-88675096-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000563475.2(SNAI3-AS1):n.2007G>C 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 0.546 in 152,096 control chromosomes in the GnomAD database, including 23,017 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 0.55 ( 23012 hom., cov: 34)

Exomes 𝑓: 0.75 ( 5 hom. )

Consequence

SNAI3-AS1
ENST00000563475.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0490

Publications

13 publications found

Variant links:

Genes affected

SNAI3-AS1 (HGNC:28327): (SNAI3 antisense RNA 1)

SNAI3-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=-0.65).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNAI3-AS1	NR_024402.2 link	n.2020G>C		non_coding_transcript_exon_variant	Exon 4 of 4
SNAI3-AS1	NR_024399.1 link	n.527+2974G>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SNAI3-AS1	ENST00000563475.2 link	n.2007G>C	non_coding_transcript_exon_variant	Exon 4 of 4	1
SNAI3-AS1	ENST00000563261.7 link	n.602+2974G>C	intron_variant	Intron 3 of 3	1
SNAI3-AS1	ENST00000568633.1 link	n.1701G>C	non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.546

AC:

83027

AN:

151962

Hom.:

23001

Cov.:

show subpopulations

Gnomad AFR

AF:

0.484

Gnomad AMI

AF:

0.453

Gnomad AMR

AF:

0.605

Gnomad ASJ

AF:

0.567

Gnomad EAS

AF:

0.739

Gnomad SAS

AF:

0.667

Gnomad FIN

AF:

0.524

Gnomad MID

AF:

0.671

Gnomad NFE

AF:

0.550

Gnomad OTH

AF:

0.589

GnomAD4 exome

AF:

0.750

AC:

AN:

Hom.:

Cov.:

AF XY:

0.667

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.875

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.625

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.550

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

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:

0.546

AC:

83071

AN:

152080

Hom.:

23012

Cov.:

AF XY:

0.549

AC XY:

40813

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.483

AC:

20034

AN:

41452

American (AMR)

AF:

0.604

AC:

9232

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.567

AC:

1968

AN:

3470

East Asian (EAS)

AF:

0.740

AC:

3825

AN:

5172

South Asian (SAS)

AF:

0.669

AC:

3222

AN:

4818

European-Finnish (FIN)

AF:

0.524

AC:

5542

AN:

10574

Middle Eastern (MID)

AF:

0.667

AC:

196

AN:

294

European-Non Finnish (NFE)

AF:

0.550

AC:

37392

AN:

67992

Other (OTH)

AF:

0.590

AC:

1247

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1967

3934

5900

7867

9834

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

734

1468

2202

2936

3670

<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:

0.403

Hom.:

1050

Bravo

AF:

0.547

Asia WGS

AF:

0.700

AC:

2431

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

(source)

DANN

Benign

0.79

PhyloP100

0.049

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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