2-199364273-G-T

Variant names:

• chr2-199364273-G-T
• rs16831366
• NM_001172509.2:c.700+4332C>A

Variant summary

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

The NM_001172509.2(SATB2):​c.700+4332C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0857 in 152,198 control chromosomes in the GnomAD database, including 630 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 0.086 (630 hom., cov: 32)
• Consequence: SATB2 NM_001172509.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.61

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=-0.52).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SATB2	NM_001172509.2	c.700+4332C>A		intron_variant	Intron 6 of 10	ENST00000417098.6	NP_001165980.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SATB2	ENST00000417098.6	c.700+4332C>A		intron_variant	Intron 6 of 10	2	NM_001172509.2	ENSP00000401112.1

Frequencies

GnomAD3 genomes AF: 0.0859 AC: 13062 AN: 152078 Hom.: 633 Cov.: 32

Gnomad AFR AF: 0.0430

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.0836

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.0857 AC: 13045 AN: 152198 Hom.: 630 Cov.: 32 AF XY: 0.0894 AC XY: 6647 AN XY: 74386

Gnomad4 AFR AF: 0.0429

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.0836

Gnomad4 OTH AF: 0.116

Alfa AF: 0.0794 Hom.: 183

Bravo AF: 0.0840

Asia WGS AF: 0.147 AC: 511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	22
DANN	Benign	0.80

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: rs16831366; hg19: chr2-200228996;