rs6039847

Positions:

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

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.84

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.10325855T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNAP25-AS1	ENST00000421143.6	n.5+42860A>G		intron_variant		5
SNAP25-AS1	ENST00000453544.5	n.62+42860A>G		intron_variant		5
SNAP25-AS1	ENST00000692436.2	n.117+42860A>G		intron_variant

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

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.0775

Gnomad4 ASJ AF: 0.0118

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.0873

Gnomad4 FIN AF: 0.0367

Gnomad4 NFE AF: 0.0377

Gnomad4 OTH AF: 0.0658

Alfa AF: 0.0400 Hom.: 260

Bravo AF: 0.0870

Asia WGS AF: 0.168 AC: 584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.9
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6039847; hg19: chr20-10306503;