rs6133852

Variant names:

• chr20-10310312-G-A
• rs6133852
• ENST00000421143.6:n.5+58403C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000421143.6(SNAP25-AS1):​n.5+58403C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0657 in 152,142 control chromosomes in the GnomAD database, including 553 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 0.066 (553 hom., cov: 32)
• Consequence: SNAP25-AS1 ENST00000421143.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNAP25-AS1	ENST00000421143.6	n.5+58403C>T		intron_variant	Intron 1 of 3	5
SNAP25-AS1	ENST00000453544.5	n.62+58403C>T		intron_variant	Intron 1 of 3	5
SNAP25-AS1	ENST00000692436.2	n.117+58403C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0657 AC: 9988 AN: 152024 Hom.: 556 Cov.: 32

Gnomad AFR AF: 0.0586

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0894

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0578

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0419

Gnomad OTH AF: 0.0685

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

GnomAD4 genome AF: 0.0657 AC: 10002 AN: 152142 Hom.: 553 Cov.: 32 AF XY: 0.0688 AC XY: 5114 AN XY: 74358

Gnomad4 AFR AF: 0.0586

Gnomad4 AMR AF: 0.0898

Gnomad4 ASJ AF: 0.0755

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0578

Gnomad4 NFE AF: 0.0419

Gnomad4 OTH AF: 0.0682

Alfa AF: 0.0520 Hom.: 142

Bravo AF: 0.0692

Asia WGS AF: 0.196 AC: 681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6133852; hg19: chr20-10290960;