3-18725912-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

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	ENST00000425799.7	n.205-20042C>T		intron_variant	Intron 3 of 8	5
SATB1-AS1	ENST00000595388.5	n.365-20042C>T		intron_variant	Intron 3 of 4	5
SATB1-AS1	ENST00000626982.2	n.196-20042C>T		intron_variant	Intron 2 of 4	5

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

Gnomad4 AFR AF: 0.0589

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.0979

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.108

Alfa AF: 0.118 Hom.: 586

Bravo AF: 0.110

Asia WGS AF: 0.106 AC: 370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4256159; hg19: chr3-18767404;