chr20-10312121-T-C

Variant names:

• chr20-10312121-T-C
• rs6032846
• ENST00000421143.7:n.132+56594A>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+56594A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 152,120 control chromosomes in the GnomAD database, including 12,322 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 0.40 (12322 hom., cov: 33)
• Consequence: SNAP25-AS1 ENST00000421143.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 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+56594A>G		intron	N/A
	SNAP25-AS1	ENST00000453544.6	TSL:5	n.62+56594A>G		intron	N/A
	SNAP25-AS1	ENST00000692436.3		n.134+56594A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60463 AN: 152002 Hom.: 12310 Cov.: 33

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.398 AC: 60515 AN: 152120 Hom.: 12322 Cov.: 33 AF XY: 0.395 AC XY: 29356 AN XY: 74368

African (AFR) AF: 0.397 AC: 16461 AN: 41470

American (AMR) AF: 0.405 AC: 6189 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1322 AN: 3468

East Asian (EAS) AF: 0.0997 AC: 516 AN: 5176

South Asian (SAS) AF: 0.300 AC: 1445 AN: 4820

European-Finnish (FIN) AF: 0.441 AC: 4663 AN: 10580

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28642 AN: 67988

Other (OTH) AF: 0.386 AC: 817 AN: 2116

Alfa AF: 0.411 Hom.: 26629

Bravo AF: 0.398

Asia WGS AF: 0.214 AC: 745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.3
DANN	Benign	0.77
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs6032846; hg19: chr20-10292769;