2-199425636-A-G

Position:

• chr2-199425636-A-G

Variant summary

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

The NM_001172509.2(SATB2):​c.346+7702T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,960 control chromosomes in the GnomAD database, including 9,556 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 0.34 (9556 hom., cov: 32)
• Consequence: SATB2 NM_001172509.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

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]

SATB2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SATB2	NM_001172509.2	c.346+7702T>C		intron_variant		ENST00000417098.6	NP_001165980.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SATB2	ENST00000417098.6	c.346+7702T>C		intron_variant		2	NM_001172509.2	ENSP00000401112.1

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50932 AN: 151842 Hom.: 9535 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.336 AC: 50993 AN: 151960 Hom.: 9556 Cov.: 32 AF XY: 0.333 AC XY: 24731 AN XY: 74260

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.615

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.355

Alfa AF: 0.289 Hom.: 10306

Bravo AF: 0.356

Asia WGS AF: 0.535 AC: 1858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.4
DANN	Benign	0.64

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: rs1992950; hg19: chr2-200290359;