Variant chr20-10070180-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000603542.6(SNAP25-AS1):n.747+34106A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 151,986 control chromosomes in the GnomAD database, including 10,901 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 0.37 ( 10901 hom., cov: 32)

Consequence

SNAP25-AS1
ENST00000603542.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.434

Variant links:

Genes affected

SNAP25-AS1 (HGNC:):

SNAP25-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNAP25-AS1	NR_040710.1 linkuse as main transcript	n.499+34106A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
SNAP25-AS1	ENST00000421143.6 linkuse as main transcript	n.234+34106A>G	intron_variant	5
SNAP25-AS1	ENST00000603542.6 linkuse as main transcript	n.747+34106A>G	intron_variant	2
SNAP25-AS1	ENST00000655307.1 linkuse as main transcript	n.628+34106A>G	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.373

AC:

56607

AN:

151866

Hom.:

10881

Cov.:

show subpopulations

Gnomad AFR

AF:

0.459

Gnomad AMI

AF:

0.265

Gnomad AMR

AF:

0.299

Gnomad ASJ

AF:

0.314

Gnomad EAS

AF:

0.356

Gnomad SAS

AF:

0.393

Gnomad FIN

AF:

0.341

Gnomad MID

AF:

0.361

Gnomad NFE

AF:

0.347

Gnomad OTH

AF:

0.358

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

GnomAD4 genome

AF:

0.373

AC:

56662

AN:

151986

Hom.:

10901

Cov.:

AF XY:

0.372

AC XY:

27639

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.459

Gnomad4 AMR

AF:

0.298

Gnomad4 ASJ

AF:

0.314

Gnomad4 EAS

AF:

0.356

Gnomad4 SAS

AF:

0.392

Gnomad4 FIN

AF:

0.341

Gnomad4 NFE

AF:

0.347

Gnomad4 OTH

AF:

0.355

Alfa

AF:

0.335

Hom.:

6946

Bravo

AF:

0.369

Asia WGS

AF:

0.378

AC:

1318

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

2.5

DANN

Benign

0.38

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over