rs13073817

Variant names:

• chr3-18665366-G-A
• rs13073817
• ENST00000595388.5:n.365-80588G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-18665366-G-A
• chr3-18665366-G-C

Variant summary

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

The ENST00000595388.5(SATB1-AS1):​n.365-80588G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 151,956 control chromosomes in the GnomAD database, including 5,408 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 0.25 (5408 hom., cov: 32)
• Consequence: SATB1-AS1 ENST00000595388.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.498

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.334 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	ENST00000595388.5	n.365-80588G>A		intron_variant	Intron 3 of 4	5
SATB1-AS1	ENST00000626982.2	n.196-80588G>A		intron_variant	Intron 2 of 4	5
SATB1-AS1	ENST00000627192.2	n.365-80588G>A		intron_variant	Intron 3 of 5	5

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37549 AN: 151836 Hom.: 5407 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.0253

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.349

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.247 AC: 37560 AN: 151956 Hom.: 5408 Cov.: 32 AF XY: 0.243 AC XY: 18053 AN XY: 74242

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.0256

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.254

Alfa AF: 0.306 Hom.: 11497

Bravo AF: 0.237

Asia WGS AF: 0.109 AC: 380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13073817; hg19: chr3-18706858;