rs362602

Variant names:

• chr20-10312880-A-G
• rs362602
• ENST00000421143.7:n.132+55835T>C

Variant summary

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

The ENST00000692436.3(SNAP25-AS1):​n.134+55835T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,078 control chromosomes in the GnomAD database, including 6,226 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 0.25 (6226 hom., cov: 32)
• Consequence: SNAP25-AS1 ENST00000692436.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 4 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000692436.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNAP25-AS1	ENST00000421143.7	TSL:5	n.132+55835T>C		intron	N/A
	SNAP25-AS1	ENST00000453544.6	TSL:5	n.62+55835T>C		intron	N/A
	SNAP25-AS1	ENST00000692436.3		n.134+55835T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38302 AN: 151960 Hom.: 6230 Cov.: 32

Gnomad AFR AF: 0.0726

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.252 AC: 38315 AN: 152078 Hom.: 6226 Cov.: 32 AF XY: 0.250 AC XY: 18586 AN XY: 74362

African (AFR) AF: 0.0728 AC: 3025 AN: 41534

American (AMR) AF: 0.250 AC: 3816 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1145 AN: 3468

East Asian (EAS) AF: 0.00231 AC: 12 AN: 5186

South Asian (SAS) AF: 0.164 AC: 790 AN: 4814

European-Finnish (FIN) AF: 0.398 AC: 4204 AN: 10564

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24390 AN: 67928

Other (OTH) AF: 0.257 AC: 542 AN: 2110

Alfa AF: 0.292 Hom.: 1310

Bravo AF: 0.236

Asia WGS AF: 0.0840 AC: 292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.9
DANN	Benign	0.51
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs362602; hg19: chr20-10293528;