rs6792314

Variant names:

• chr3-18632501-A-G
• rs6792314
• ENST00000595388.5:n.364+105175A>G

Variant summary

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

The ENST00000595388.5(SATB1-AS1):​n.364+105175A>G variant causes a intron 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 ENST00000595388.5 intron
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SATB1-AS1	ENST00000595388.5	n.364+105175A>G		intron_variant	Intron 3 of 4	5
SATB1-AS1	ENST00000626982.2	n.195+105175A>G		intron_variant	Intron 2 of 4	5
SATB1-AS1	ENST00000627192.2	n.364+105175A>G		intron_variant	Intron 3 of 5	5

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;