rs660454

Variant names:

• chr20-10070180-T-C
• rs660454
• ENST00000421143.7:n.361+34106A>G

Your query was ambiguous. Multiple possible variants found:

• chr20-10070180-T-C
• chr20-10070180-T-G

Variant summary

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

The ENST00000603542.6(SNAP25-AS1):​n.747+34106A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 151,986 control chromosomes in the GnomAD database, including 10,901 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 0.37 (10901 hom., cov: 32)
• Consequence: SNAP25-AS1 ENST00000603542.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000603542.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNAP25-AS1	NR_040710.1		n.499+34106A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNAP25-AS1	ENST00000421143.7	TSL:5	n.361+34106A>G		intron	N/A
	SNAP25-AS1	ENST00000603542.6	TSL:2	n.747+34106A>G		intron	N/A
	SNAP25-AS1	ENST00000655307.1		n.628+34106A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56607 AN: 151866 Hom.: 10881 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.373 AC: 56662 AN: 151986 Hom.: 10901 Cov.: 32 AF XY: 0.372 AC XY: 27639 AN XY: 74258

African (AFR) AF: 0.459 AC: 19040 AN: 41442

American (AMR) AF: 0.298 AC: 4553 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1090 AN: 3470

East Asian (EAS) AF: 0.356 AC: 1835 AN: 5156

South Asian (SAS) AF: 0.392 AC: 1886 AN: 4816

European-Finnish (FIN) AF: 0.341 AC: 3601 AN: 10572

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23563 AN: 67958

Other (OTH) AF: 0.355 AC: 750 AN: 2114

Alfa AF: 0.339 Hom.: 9595

Bravo AF: 0.369

Asia WGS AF: 0.378 AC: 1318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.5
DANN	Benign	0.38
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs660454; hg19: chr20-10050828;