ENST00000425799.7:n.205-20042C>T

Variant names:

• chr3-18725912-C-T
• rs4256159
• ENST00000425799.7:n.205-20042C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000425799.7(SATB1-AS1):​n.205-20042C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,060 control chromosomes in the GnomAD database, including 1,089 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 0.11 (1089 hom., cov: 32)
• Consequence: SATB1-AS1 ENST00000425799.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.19
• Publications: 36 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425799.7. 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	ENST00000425799.7	TSL:5	n.205-20042C>T		intron	N/A
	SATB1-AS1	ENST00000595388.5	TSL:5	n.365-20042C>T		intron	N/A
	SATB1-AS1	ENST00000626982.2	TSL:5	n.196-20042C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17321 AN: 151942 Hom.: 1089 Cov.: 32

Gnomad AFR AF: 0.0590

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.0978

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.114 AC: 17326 AN: 152060 Hom.: 1089 Cov.: 32 AF XY: 0.112 AC XY: 8318 AN XY: 74312

African (AFR) AF: 0.0589 AC: 2445 AN: 41476

American (AMR) AF: 0.110 AC: 1673 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 500 AN: 3472

East Asian (EAS) AF: 0.137 AC: 710 AN: 5166

South Asian (SAS) AF: 0.0979 AC: 471 AN: 4810

European-Finnish (FIN) AF: 0.111 AC: 1174 AN: 10586

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9947 AN: 67966

Other (OTH) AF: 0.108 AC: 227 AN: 2106

Alfa AF: 0.129 Hom.: 2747

Bravo AF: 0.110

Asia WGS AF: 0.106 AC: 370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	20
DANN	Benign	0.73
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs4256159; hg19: chr3-18767404;