rs6039847

Variant names:

• chr20-10325855-T-C
• rs6039847
• ENST00000421143.7:n.132+42860A>G

Your query was ambiguous. Multiple possible variants found:

• chr20-10325855-T-C
• chr20-10325855-T-G

Variant summary

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

The ENST00000692436.3(SNAP25-AS1):​n.134+42860A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0798 in 152,148 control chromosomes in the GnomAD database, including 795 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 0.080 (795 hom., cov: 32)
• Consequence: SNAP25-AS1 ENST00000692436.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.84
• Publications: 3 publications found

Genes affected

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

ENSG00000305016 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000692436.3. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNAP25-AS1	ENST00000421143.7	TSL:5	n.132+42860A>G		intron	N/A
	SNAP25-AS1	ENST00000453544.6	TSL:5	n.62+42860A>G		intron	N/A
	SNAP25-AS1	ENST00000692436.3		n.134+42860A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0796 AC: 12109 AN: 152028 Hom.: 795 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0769

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.0870

Gnomad FIN AF: 0.0367

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0377

Gnomad OTH AF: 0.0660

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

GnomAD4 genome AF: 0.0798 AC: 12135 AN: 152148 Hom.: 795 Cov.: 32 AF XY: 0.0804 AC XY: 5979 AN XY: 74362

African (AFR) AF: 0.145 AC: 6012 AN: 41504

American (AMR) AF: 0.0775 AC: 1184 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0118 AC: 41 AN: 3468

East Asian (EAS) AF: 0.267 AC: 1377 AN: 5152

South Asian (SAS) AF: 0.0873 AC: 421 AN: 4824

European-Finnish (FIN) AF: 0.0367 AC: 388 AN: 10586

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0377 AC: 2564 AN: 68010

Other (OTH) AF: 0.0658 AC: 139 AN: 2114

Alfa AF: 0.0442 Hom.: 405

Bravo AF: 0.0870

Asia WGS AF: 0.168 AC: 584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.9
DANN	Benign	0.33
PhyloP100		1.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6039847;

hg19: chr20-10306503;