chr3-18632501-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000595388.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SATB1-AS1	ENST00000595388.5	TSL:5	n.364+105175A>G		intron	N/A
	SATB1-AS1	ENST00000626982.2	TSL:5	n.195+105175A>G		intron	N/A
	SATB1-AS1	ENST00000627192.2	TSL:5	n.364+105175A>G		intron	N/A

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

African (AFR) AF: 0.191 AC: 7911 AN: 41498

American (AMR) AF: 0.231 AC: 3515 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1036 AN: 3464

East Asian (EAS) AF: 0.0322 AC: 165 AN: 5122

South Asian (SAS) AF: 0.253 AC: 1218 AN: 4816

European-Finnish (FIN) AF: 0.282 AC: 2980 AN: 10580

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.341 AC: 23171 AN: 67876

Other (OTH) AF: 0.270 AC: 570 AN: 2110

Alfa AF: 0.315 Hom.: 30362

Bravo AF: 0.263

Asia WGS AF: 0.130 AC: 454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.32
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs6792314; hg19: chr3-18673993;