rs334960

Variant names:

• chr3-18569385-C-T
• rs334960
• ENST00000456253.6:n.610-16002C>T

Variant summary

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

The ENST00000683051.1(SATB1-AS1):​n.120+42059C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,730 control chromosomes in the GnomAD database, including 8,828 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 0.31 (8828 hom., cov: 31)
• Consequence: SATB1-AS1 ENST00000683051.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 7 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000683051.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SATB1-AS1	ENST00000456253.6	TSL:5	n.610-16002C>T		intron	N/A
	SATB1-AS1	ENST00000595250.5	TSL:5	n.462-16235C>T		intron	N/A
	SATB1-AS1	ENST00000595388.5	TSL:5	n.364+42059C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47759 AN: 151612 Hom.: 8824 Cov.: 31

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.315 AC: 47782 AN: 151730 Hom.: 8828 Cov.: 31 AF XY: 0.316 AC XY: 23453 AN XY: 74134

African (AFR) AF: 0.120 AC: 4975 AN: 41428

American (AMR) AF: 0.276 AC: 4203 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1233 AN: 3466

East Asian (EAS) AF: 0.266 AC: 1369 AN: 5140

South Asian (SAS) AF: 0.328 AC: 1578 AN: 4810

European-Finnish (FIN) AF: 0.473 AC: 4981 AN: 10532

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28252 AN: 67834

Other (OTH) AF: 0.321 AC: 676 AN: 2104

Alfa AF: 0.390 Hom.: 6415

Bravo AF: 0.293

Asia WGS AF: 0.313 AC: 1086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.34
DANN	Benign	0.18
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs334960; hg19: chr3-18610877;