rs674630

Positions:

• chr20-10064430-G-T

Variant summary

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

The NR_040710.1(SNAP25-AS1):​n.500-37782C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 151,936 control chromosomes in the GnomAD database, including 20,010 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 0.51 (20010 hom., cov: 32)
• Consequence: SNAP25-AS1 NR_040710.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNAP25-AS1	NR_040710.1	n.500-37782C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNAP25-AS1	ENST00000421143.6	n.235-37782C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77369 AN: 151818 Hom.: 19993 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.510 AC: 77429 AN: 151936 Hom.: 20010 Cov.: 32 AF XY: 0.508 AC XY: 37734 AN XY: 74252

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.493

Alfa AF: 0.547 Hom.: 30589

Bravo AF: 0.502

Asia WGS AF: 0.343 AC: 1195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs674630; hg19: chr20-10045078;