Genetic Variant SNAP25-AS1:n.132+55835T>C (chr20-10312880-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 ENST00000421143.7(SNAP25-AS1):n.132+55835T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,078 control chromosomes in the GnomAD database, including 6,226 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 0.25 ( 6226 hom., cov: 32)

Consequence

SNAP25-AS1
ENST00000421143.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.25

Publications

4 publications found

Variant links:

Genes affected

SNAP25-AS1 (HGNC:44312): (SNAP25 antisense RNA 1)

SNAP25-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=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SNAP25-AS1	ENST00000421143.7 link	n.132+55835T>C	intron_variant	Intron 1 of 3	5
SNAP25-AS1	ENST00000453544.6 link	n.62+55835T>C	intron_variant	Intron 1 of 4	5
SNAP25-AS1	ENST00000692436.3 link	n.134+55835T>C	intron_variant	Intron 1 of 2
SNAP25-AS1	ENST00000807507.1 link	n.109+55835T>C	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.252

AC:

38302

AN:

151960

Hom.:

6230

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0726

Gnomad AMI

AF:

0.346

Gnomad AMR

AF:

0.250

Gnomad ASJ

AF:

0.330

Gnomad EAS

AF:

0.00231

Gnomad SAS

AF:

0.163

Gnomad FIN

AF:

0.398

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.359

Gnomad OTH

AF:

0.259

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

GnomAD4 genome

AF:

0.252

AC:

38315

AN:

152078

Hom.:

6226

Cov.:

AF XY:

0.250

AC XY:

18586

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.0728

AC:

3025

AN:

41534

American (AMR)

AF:

0.250

AC:

3816

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.330

AC:

1145

AN:

3468

East Asian (EAS)

AF:

0.00231

AC:

AN:

5186

South Asian (SAS)

AF:

0.164

AC:

790

AN:

4814

European-Finnish (FIN)

AF:

0.398

AC:

4204

AN:

10564

Middle Eastern (MID)

AF:

0.259

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.359

AC:

24390

AN:

67928

Other (OTH)

AF:

0.257

AC:

542

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1344

2688

4031

5375

6719

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

388

776

1164

1552

1940

<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:

0.292

Hom.:

1310

Bravo

AF:

0.236

Asia WGS

AF:

0.0840

AC:

292

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

9.9

(source)

DANN

Benign

0.51

PhyloP100

1.2

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