ENST00000456253.6:n.609+13030G>T

Variant names:

• chr3-18540356-G-T
• rs7633075
• ENST00000456253.6:n.609+13030G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000456253.6(SATB1-AS1):​n.609+13030G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,044 control chromosomes in the GnomAD database, including 5,642 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 0.23 (5642 hom., cov: 32)
• Consequence: SATB1-AS1 ENST00000456253.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.315
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456253.6. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SATB1-AS1	ENST00000456253.6	TSL:5	n.609+13030G>T		intron	N/A
	SATB1-AS1	ENST00000595250.5	TSL:5	n.461+13030G>T		intron	N/A
	SATB1-AS1	ENST00000595388.5	TSL:5	n.364+13030G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35422 AN: 151926 Hom.: 5618 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.233 AC: 35493 AN: 152044 Hom.: 5642 Cov.: 32 AF XY: 0.238 AC XY: 17694 AN XY: 74320

African (AFR) AF: 0.413 AC: 17114 AN: 41452

American (AMR) AF: 0.326 AC: 4987 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 563 AN: 3470

East Asian (EAS) AF: 0.354 AC: 1828 AN: 5160

South Asian (SAS) AF: 0.232 AC: 1119 AN: 4816

European-Finnish (FIN) AF: 0.183 AC: 1932 AN: 10584

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7358 AN: 67972

Other (OTH) AF: 0.209 AC: 442 AN: 2110

Alfa AF: 0.145 Hom.: 3991

Bravo AF: 0.252

Asia WGS AF: 0.307 AC: 1063 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.5
DANN	Benign	0.58
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs7633075; hg19: chr3-18581848; COSMIC: COSV69863005;