rs9838549

Variant names:

• chr3-18567853-A-G
• rs9838549
• ENST00000456253.6:n.610-17534A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000456253.6(SATB1-AS1):​n.610-17534A>G variant causes a intron 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 ENST00000456253.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SATB1-AS1	ENST00000456253.6	n.610-17534A>G		intron_variant	Intron 5 of 6	5
SATB1-AS1	ENST00000595250.5	n.462-17767A>G		intron_variant	Intron 4 of 4	5
SATB1-AS1	ENST00000595388.5	n.364+40527A>G		intron_variant	Intron 3 of 4	5

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

African (AFR) AF: 0.513 AC: 21194 AN: 41330

American (AMR) AF: 0.340 AC: 5176 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1156 AN: 3462

East Asian (EAS) AF: 0.241 AC: 1234 AN: 5114

South Asian (SAS) AF: 0.326 AC: 1564 AN: 4802

European-Finnish (FIN) AF: 0.314 AC: 3311 AN: 10544

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24239 AN: 67830

Other (OTH) AF: 0.384 AC: 808 AN: 2104

Alfa AF: 0.374 Hom.: 14213

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
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs9838549; hg19: chr3-18609345;