rs13073817

Positions:

• 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 ENST00000683051.1(SATB1-AS1):​n.121-80588G>A 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 0.247 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 ENST00000683051.1 intron, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SATB1-AS1	ENST00000683051.1	n.121-80588G>A		intron_variant, non_coding_transcript_variant

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;