chr20-10214030-G-A

Position:

• chr20-10214030-G-A

Variant summary

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

The ENST00000451151.6(SNAP25-AS1):​n.295+5207C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 151,998 control chromosomes in the GnomAD database, including 4,460 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 0.23 (4460 hom., cov: 32)
• Consequence: SNAP25-AS1 ENST00000451151.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.647

Genes affected

SNAP25-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNAP25-AS1	NR_040710.1	n.270+5207C>T		intron_variant
LOC124904959	XR_007067723.1	n.376+175G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNAP25-AS1	ENST00000421143.6	n.6-17093C>T		intron_variant		5
SNAP25-AS1	ENST00000426491.5	n.270+5207C>T		intron_variant		5
SNAP25-AS1	ENST00000451151.6	n.295+5207C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35584 AN: 151880 Hom.: 4455 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.00675

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.234 AC: 35602 AN: 151998 Hom.: 4460 Cov.: 32 AF XY: 0.227 AC XY: 16879 AN XY: 74286

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.00677

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.273

Alfa AF: 0.265 Hom.: 7454

Bravo AF: 0.233

Asia WGS AF: 0.102 AC: 357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.2
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8119844; hg19: chr20-10194678;