rs4973706

Variant names:

• chr3-18880280-T-C
• rs4973706
• ENST00000425799.7:n.464-26421T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-18880280-T-C
• chr3-18880280-T-G

Variant summary

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

The ENST00000425799.7(SATB1-AS1):​n.464-26421T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 151,914 control chromosomes in the GnomAD database, including 10,175 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 (10175 hom., cov: 32)
• Consequence: SATB1-AS1 ENST00000425799.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00
• Publications: 5 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.584 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	ENST00000425799.7	n.464-26421T>C		intron_variant	Intron 6 of 8	5
SATB1-AS1	ENST00000626982.2	n.352-22224T>C		intron_variant	Intron 4 of 4	5
SATB1-AS1	ENST00000630271.2	n.469-26421T>C		intron_variant	Intron 6 of 7	5

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50080 AN: 151794 Hom.: 10151 Cov.: 32

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.330 AC: 50157 AN: 151914 Hom.: 10175 Cov.: 32 AF XY: 0.322 AC XY: 23927 AN XY: 74256

African (AFR) AF: 0.590 AC: 24454 AN: 41416

American (AMR) AF: 0.255 AC: 3888 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 797 AN: 3468

East Asian (EAS) AF: 0.229 AC: 1182 AN: 5162

South Asian (SAS) AF: 0.217 AC: 1046 AN: 4822

European-Finnish (FIN) AF: 0.153 AC: 1615 AN: 10572

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16284 AN: 67920

Other (OTH) AF: 0.285 AC: 600 AN: 2108

Alfa AF: 0.270 Hom.: 19437

Bravo AF: 0.349

Asia WGS AF: 0.229 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.11
DANN	Benign	0.63
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs4973706; hg19: chr3-18921772;