rs1822120

chr3-18495061-T-C

Variant summary

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

The NR_125803.1(SATB1-AS1):n.402+29022T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 151,968 control chromosomes in the GnomAD database, including 8,223 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 0.33 (8223 hom., cov: 32)
• Consequence: SATB1-AS1 NR_125803.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.655

Genes affected

SATB1-AS1 (HGNC:50687): (SATB1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SATB1-AS1	NR_125803.1	n.402+29022T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SATB1-AS1	ENST00000414198.7	n.615+29022T>C		intron_variant, non_coding_transcript_variant		2
SATB1-AS1	ENST00000438418.8	n.776+29022T>C		intron_variant, non_coding_transcript_variant		5
SATB1-AS1	ENST00000456253.6	n.302+21203T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49534 AN: 151850 Hom.: 8213 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.326 AC: 49576 AN: 151968 Hom.: 8223 Cov.: 32 AF XY: 0.331 AC XY: 24573 AN XY: 74242

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.302

Alfa AF: 0.305 Hom.: 13165

Bravo AF: 0.326

Asia WGS AF: 0.376 AC: 1308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	16
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1822120; hg19: chr3-18536553;