rs9838549

chr3-18567853-A-G

Variant summary

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

The ENST00000683051.1(SATB1-AS1):n.120+40527A>G 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 0.39 in 151,598 control chromosomes in the GnomAD database, including 11,970 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 0.39 (11970 hom., cov: 30)
• Consequence: SATB1-AS1 ENST00000683051.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SATB1-AS1	ENST00000683051.1	n.120+40527A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59075 AN: 151480 Hom.: 11949 Cov.: 30

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.390 AC: 59128 AN: 151598 Hom.: 11970 Cov.: 30 AF XY: 0.385 AC XY: 28497 AN XY: 74066

Gnomad4 AFR AF: 0.513

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.384

Alfa AF: 0.372 Hom.: 9314

Bravo AF: 0.400

Asia WGS AF: 0.283 AC: 984 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.079
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9838549; hg19: chr3-18609345;