rs6032846

chr20-10312121-T-C

Variant summary

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

The ENST00000421143.6(SNAP25-AS1):n.5+56594A>G 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 0.398 in 152,120 control chromosomes in the GnomAD database, including 12,322 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 0.40 (12322 hom., cov: 33)
• Consequence: SNAP25-AS1 ENST00000421143.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNAP25-AS1	ENST00000421143.6	n.5+56594A>G		intron_variant, non_coding_transcript_variant		5
SNAP25-AS1	ENST00000453544.5	n.62+56594A>G		intron_variant, non_coding_transcript_variant		5
SNAP25-AS1	ENST00000692436.2	n.117+56594A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60463 AN: 152002 Hom.: 12310 Cov.: 33

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.398 AC: 60515 AN: 152120 Hom.: 12322 Cov.: 33 AF XY: 0.395 AC XY: 29356 AN XY: 74368

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.0997

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.386

Alfa AF: 0.414 Hom.: 5236

Bravo AF: 0.398

Asia WGS AF: 0.214 AC: 745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	6.3
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6032846; hg19: chr20-10292769;