rs362605

Variant names:

• chr20-10316472-T-C
• rs362605
• ENST00000421143.6:n.5+52243A>G

Variant summary

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

The ENST00000421143.6(SNAP25-AS1):​n.5+52243A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0406 in 152,282 control chromosomes in the GnomAD database, including 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 0.041 (322 hom., cov: 32)
• Consequence: SNAP25-AS1 ENST00000421143.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.588

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.107 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
SNAP25-AS1	ENST00000421143.6	n.5+52243A>G		intron_variant	Intron 1 of 3	5
SNAP25-AS1	ENST00000453544.5	n.62+52243A>G		intron_variant	Intron 1 of 3	5
SNAP25-AS1	ENST00000692436.2	n.117+52243A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0405 AC: 6158 AN: 152164 Hom.: 319 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0372

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00435

Gnomad FIN AF: 0.000847

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0116

Gnomad OTH AF: 0.0459

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

GnomAD4 genome AF: 0.0406 AC: 6182 AN: 152282 Hom.: 322 Cov.: 32 AF XY: 0.0397 AC XY: 2954 AN XY: 74464

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.0372

Gnomad4 ASJ AF: 0.0300

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00456

Gnomad4 FIN AF: 0.000847

Gnomad4 NFE AF: 0.0116

Gnomad4 OTH AF: 0.0455

Alfa AF: 0.0262 Hom.: 15

Bravo AF: 0.0459

Asia WGS AF: 0.00549 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.8
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs362605; hg19: chr20-10297120;