rs6809854

Variant names:

• chr3-18742931-A-G
• rs6809854
• ENST00000425799.7:n.205-3023A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-18742931-A-G
• chr3-18742931-A-T

Variant summary

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

The ENST00000683051.1(SATB1-AS1):​n.121-3023A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 151,920 control chromosomes in the GnomAD database, including 2,979 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 0.19 (2979 hom., cov: 32)
• Consequence: SATB1-AS1 ENST00000683051.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 22 publications found

Genes affected

SATB1-AS1 (HGNC:50687): (SATB1 antisense RNA 1)

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 (AMR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000683051.1. 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
	SATB1-AS1	ENST00000425799.7	TSL:5	n.205-3023A>G		intron	N/A
	SATB1-AS1	ENST00000595388.5	TSL:5	n.365-3023A>G		intron	N/A
	SATB1-AS1	ENST00000626982.2	TSL:5	n.196-3023A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29496 AN: 151802 Hom.: 2976 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0927

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.194 AC: 29515 AN: 151920 Hom.: 2979 Cov.: 32 AF XY: 0.195 AC XY: 14508 AN XY: 74250

African (AFR) AF: 0.184 AC: 7650 AN: 41470

American (AMR) AF: 0.250 AC: 3815 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 671 AN: 3468

East Asian (EAS) AF: 0.0931 AC: 478 AN: 5134

South Asian (SAS) AF: 0.183 AC: 885 AN: 4824

European-Finnish (FIN) AF: 0.191 AC: 2022 AN: 10580

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13268 AN: 67898

Other (OTH) AF: 0.199 AC: 419 AN: 2108

Alfa AF: 0.198 Hom.: 11970

Bravo AF: 0.201

Asia WGS AF: 0.120 AC: 414 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.8
DANN	Benign	0.64
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs6809854; hg19: chr3-18784423;