20-10313948-G-C

Variant names:

• chr20-10313948-G-C
• rs1984830
• ENST00000421143.7:n.132+54767C>G

Variant summary

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

The ENST00000421143.7(SNAP25-AS1):​n.132+54767C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 151,928 control chromosomes in the GnomAD database, including 5,751 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 0.26 (5751 hom., cov: 32)
• Consequence: SNAP25-AS1 ENST00000421143.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.864
• Publications: 2 publications found

Genes affected

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

ENSG00000286936 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.324 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNAP25-AS1	ENST00000421143.7	TSL:5	n.132+54767C>G		intron	N/A
	SNAP25-AS1	ENST00000453544.6	TSL:5	n.62+54767C>G		intron	N/A
	SNAP25-AS1	ENST00000692436.3		n.134+54767C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39754 AN: 151810 Hom.: 5746 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.00619

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.262 AC: 39790 AN: 151928 Hom.: 5751 Cov.: 32 AF XY: 0.257 AC XY: 19109 AN XY: 74210

African (AFR) AF: 0.179 AC: 7418 AN: 41440

American (AMR) AF: 0.263 AC: 4017 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1200 AN: 3470

East Asian (EAS) AF: 0.00621 AC: 32 AN: 5156

South Asian (SAS) AF: 0.229 AC: 1100 AN: 4800

European-Finnish (FIN) AF: 0.265 AC: 2788 AN: 10528

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22291 AN: 67956

Other (OTH) AF: 0.275 AC: 580 AN: 2110

Alfa AF: 0.180 Hom.: 390

Bravo AF: 0.258

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.1
DANN	Benign	0.64
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs1984830; hg19: chr20-10294596;