rs6133852

Positions:

• chr20-10310312-G-A

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNAP25-AS1	ENST00000421143.6	n.5+58403C>T		intron_variant, non_coding_transcript_variant		5
SNAP25-AS1	ENST00000453544.5	n.62+58403C>T		intron_variant, non_coding_transcript_variant		5
SNAP25-AS1	ENST00000692436.2	n.117+58403C>T		intron_variant, non_coding_transcript_variant

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;