rs13028839

chr2-199370629-G-Achr2-199370629-G-T

Variant summary

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

The NM_001172509.2(SATB2):c.598-1922C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0785 in 151,940 control chromosomes in the GnomAD database, including 563 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 0.079 (563 hom., cov: 30)
• Consequence: SATB2 NM_001172509.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.29

Genes affected

SATB2 (HGNC:21637): (SATB homeobox 2) This gene encodes a DNA binding protein that specifically binds nuclear matrix attachment regions. The encoded protein is involved in transcription regulation and chromatin remodeling. Defects in this gene are associated with isolated cleft palate and cognitive disability. Alternate splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Feb 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SATB2	NM_001172509.2	c.598-1922C>T		intron_variant		ENST00000417098.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SATB2	ENST00000417098.6	c.598-1922C>T		intron_variant		2	NM_001172509.2	P1

Frequencies

GnomAD3 genomes AF: 0.0786 AC: 11931 AN: 151822 Hom.: 563 Cov.: 30

Gnomad AFR AF: 0.0224

Gnomad AMI AF: 0.0945

Gnomad AMR AF: 0.0913

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.0380

Gnomad FIN AF: 0.0736

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0852

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

GnomAD4 genome AF: 0.0785 AC: 11928 AN: 151940 Hom.: 563 Cov.: 30 AF XY: 0.0763 AC XY: 5667 AN XY: 74252

Gnomad4 AFR AF: 0.0223

Gnomad4 AMR AF: 0.0916

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.0379

Gnomad4 FIN AF: 0.0736

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.0843

Alfa AF: 0.0924 Hom.: 326

Bravo AF: 0.0821

Asia WGS AF: 0.0720 AC: 251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.11
Dann	Benign	0.60

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs13028839; hg19: chr2-200235352;