rs362552

Variant names:

• chr20-10315569-A-G
• rs362552
• ENST00000808005.1:n.144T>C

Variant summary

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

The ENST00000808005.1(ENSG00000286936):​n.144T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,720 control chromosomes in the GnomAD database, including 10,087 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 0.36 (10087 hom., cov: 30)
• Consequence: ENSG00000286936 ENST00000808005.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.555
• Publications: 3 publications found

Genes affected

ENSG00000286936 (HGNC:):

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.433 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
ENSG00000286936	ENST00000808005.1	n.144T>C		non_coding_transcript_exon_variant	Exon 2 of 4
ENSG00000286936	ENST00000808006.1	n.157T>C		non_coding_transcript_exon_variant	Exon 2 of 4
ENSG00000286936	ENST00000808007.1	n.118T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54650 AN: 151604 Hom.: 10084 Cov.: 30

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.360 AC: 54678 AN: 151720 Hom.: 10087 Cov.: 30 AF XY: 0.358 AC XY: 26504 AN XY: 74126

African (AFR) AF: 0.439 AC: 18126 AN: 41308

American (AMR) AF: 0.322 AC: 4915 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1160 AN: 3464

East Asian (EAS) AF: 0.408 AC: 2102 AN: 5150

South Asian (SAS) AF: 0.370 AC: 1777 AN: 4802

European-Finnish (FIN) AF: 0.262 AC: 2750 AN: 10500

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22845 AN: 67934

Other (OTH) AF: 0.332 AC: 702 AN: 2114

Alfa AF: 0.346 Hom.: 4832

Bravo AF: 0.367

Asia WGS AF: 0.367 AC: 1276 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	3.5
DANN	Benign	0.59
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs362552; hg19: chr20-10296217;