rs6809854

Positions:

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

Variant summary

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

The ENST00000683051.1(SATB1-AS1):​n.121-3023A>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

Genes affected

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

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SATB1-AS1	ENST00000683051.1	n.121-3023A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.0931

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.199

Alfa AF: 0.200 Hom.: 5531

Bravo AF: 0.201

Asia WGS AF: 0.120 AC: 414 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6809854; hg19: chr3-18784423;