rs17199393

Positions:

• chr2-199381975-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001172509.2(SATB2):​c.347-155C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0375 in 152,264 control chromosomes in the GnomAD database, including 136 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 0.037 (136 hom., cov: 32)
• Consequence: SATB2 NM_001172509.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SATB2	NM_001172509.2	c.347-155C>T		intron_variant		ENST00000417098.6	NP_001165980.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SATB2	ENST00000417098.6	c.347-155C>T		intron_variant		2	NM_001172509.2	ENSP00000401112.1

Frequencies

GnomAD3 genomes AF: 0.0375 AC: 5710 AN: 152146 Hom.: 136 Cov.: 32

Gnomad AFR AF: 0.00960

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0523

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0559

Gnomad FIN AF: 0.0150

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0522

Gnomad OTH AF: 0.0535

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

GnomAD4 genome AF: 0.0375 AC: 5705 AN: 152264 Hom.: 136 Cov.: 32 AF XY: 0.0363 AC XY: 2700 AN XY: 74444

Gnomad4 AFR AF: 0.00958

Gnomad4 AMR AF: 0.0522

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0564

Gnomad4 FIN AF: 0.0150

Gnomad4 NFE AF: 0.0522

Gnomad4 OTH AF: 0.0530

Alfa AF: 0.0485 Hom.: 63

Bravo AF: 0.0380

Asia WGS AF: 0.0210 AC: 72 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	18
DANN	Benign	0.82

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: rs17199393; hg19: chr2-200246698;