rs6792314

Positions:

• chr3-18632501-A-G

Variant summary

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

The ENST00000683051.1(SATB1-AS1):​n.120+105175A>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 0.27 in 151,904 control chromosomes in the GnomAD database, including 6,057 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 0.27 (6057 hom., cov: 32)
• Consequence: SATB1-AS1 ENST00000683051.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.563

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=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 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.120+105175A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41046 AN: 151788 Hom.: 6054 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.0319

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.270 AC: 41069 AN: 151904 Hom.: 6057 Cov.: 32 AF XY: 0.266 AC XY: 19713 AN XY: 74218

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.0322

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.270

Alfa AF: 0.323 Hom.: 14545

Bravo AF: 0.263

Asia WGS AF: 0.130 AC: 454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6792314; hg19: chr3-18673993;