20-10083881-A-G

Variant names:

• chr20-10083881-A-G
• rs551927
• ENST00000421143.7:n.361+20405T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000421143.7(SNAP25-AS1):​n.361+20405T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 151,964 control chromosomes in the GnomAD database, including 16,143 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 0.45 (16143 hom., cov: 32)
• Consequence: SNAP25-AS1 ENST00000421143.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421143.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNAP25-AS1	NR_040710.1		n.499+20405T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNAP25-AS1	ENST00000421143.7	TSL:5	n.361+20405T>C		intron	N/A
	SNAP25-AS1	ENST00000426491.5	TSL:5	n.500-6968T>C		intron	N/A
	SNAP25-AS1	ENST00000453544.6	TSL:5	n.428-6968T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68773 AN: 151848 Hom.: 16123 Cov.: 32

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.453 AC: 68826 AN: 151964 Hom.: 16143 Cov.: 32 AF XY: 0.457 AC XY: 33960 AN XY: 74270

African (AFR) AF: 0.573 AC: 23763 AN: 41450

American (AMR) AF: 0.359 AC: 5478 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1246 AN: 3468

East Asian (EAS) AF: 0.552 AC: 2846 AN: 5156

South Asian (SAS) AF: 0.547 AC: 2637 AN: 4818

European-Finnish (FIN) AF: 0.453 AC: 4786 AN: 10562

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.393 AC: 26710 AN: 67948

Other (OTH) AF: 0.429 AC: 907 AN: 2112

Alfa AF: 0.411 Hom.: 36073

Bravo AF: 0.446

Asia WGS AF: 0.551 AC: 1918 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.027
DANN	Benign	0.46
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs551927; hg19: chr20-10064529;