rs2210585

Variant names:

• chr20-10148952-A-G
• rs2210585
• ENST00000421143.7:n.253-44558T>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.253-44558T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 152,134 control chromosomes in the GnomAD database, including 34,540 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 0.66 (34540 hom., cov: 33)
• Consequence: SNAP25-AS1 ENST00000421143.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.585
• Publications: 6 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNAP25-AS1	NR_040710.1	n.391-44558T>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNAP25-AS1	ENST00000421143.7	n.253-44558T>C		intron_variant	Intron 2 of 3	5
SNAP25-AS1	ENST00000426491.5	n.391-44558T>C		intron_variant	Intron 2 of 4	5
SNAP25-AS1	ENST00000451151.7	n.422-44558T>C		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.663 AC: 100789 AN: 152014 Hom.: 34490 Cov.: 33

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.663 AC: 100891 AN: 152134 Hom.: 34540 Cov.: 33 AF XY: 0.659 AC XY: 48994 AN XY: 74360

African (AFR) AF: 0.808 AC: 33552 AN: 41522

American (AMR) AF: 0.542 AC: 8276 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1742 AN: 3468

East Asian (EAS) AF: 0.321 AC: 1659 AN: 5170

South Asian (SAS) AF: 0.564 AC: 2717 AN: 4818

European-Finnish (FIN) AF: 0.706 AC: 7468 AN: 10572

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43443 AN: 67986

Other (OTH) AF: 0.641 AC: 1353 AN: 2110

Alfa AF: 0.636 Hom.: 139901

Bravo AF: 0.655

Asia WGS AF: 0.456 AC: 1593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.36
DANN	Benign	0.43
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs2210585; hg19: chr20-10129600;