3-18665366-G-A

Variant names:

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

Variant summary

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

The ENST00000683051.1(SATB1-AS1):​n.121-80588G>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 ENST00000683051.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.498
• Publications: 33 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.334 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	ENST00000595388.5	TSL:5	n.365-80588G>A		intron	N/A
	SATB1-AS1	ENST00000626982.2	TSL:5	n.196-80588G>A		intron	N/A
	SATB1-AS1	ENST00000627192.2	TSL:5	n.365-80588G>A		intron	N/A

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

African (AFR) AF: 0.121 AC: 5000 AN: 41460

American (AMR) AF: 0.219 AC: 3350 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1015 AN: 3468

East Asian (EAS) AF: 0.0256 AC: 132 AN: 5162

South Asian (SAS) AF: 0.235 AC: 1130 AN: 4812

European-Finnish (FIN) AF: 0.282 AC: 2967 AN: 10534

Middle Eastern (MID) AF: 0.345 AC: 100 AN: 290

European-Non Finnish (NFE) AF: 0.338 AC: 22953 AN: 67940

Other (OTH) AF: 0.254 AC: 535 AN: 2110

Alfa AF: 0.299 Hom.: 25593

Bravo AF: 0.237

Asia WGS AF: 0.109 AC: 380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.84
PhyloP100		-0.50

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13073817;

hg19: chr3-18706858;