rs78025867

Variant names:

• chr3-18577361-A-T
• rs78025867
• ENST00000456253.6:n.610-8026A>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+50035A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0491 in 152,252 control chromosomes in the GnomAD database, including 516 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 0.049 (516 hom., cov: 32)
• Consequence: SATB1-AS1 ENST00000683051.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185
• Publications: 0 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 (AFR) allele frequency at 95% confidence interval = 0.155 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.610-8026A>T		intron	N/A
	SATB1-AS1	ENST00000595250.5	TSL:5	n.462-8259A>T		intron	N/A
	SATB1-AS1	ENST00000595388.5	TSL:5	n.364+50035A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0490 AC: 7452 AN: 152134 Hom.: 514 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0312

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00357

Gnomad OTH AF: 0.0497

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

GnomAD4 genome AF: 0.0491 AC: 7469 AN: 152252 Hom.: 516 Cov.: 32 AF XY: 0.0479 AC XY: 3566 AN XY: 74452

African (AFR) AF: 0.158 AC: 6574 AN: 41522

American (AMR) AF: 0.0311 AC: 476 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00807 AC: 28 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.00145 AC: 7 AN: 4824

European-Finnish (FIN) AF: 0.000188 AC: 2 AN: 10632

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.00357 AC: 243 AN: 68012

Other (OTH) AF: 0.0491 AC: 104 AN: 2116

Alfa AF: 0.0292 Hom.: 40

Bravo AF: 0.0566

Asia WGS AF: 0.0110 AC: 38 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	5.0
DANN	Benign	0.78
PhyloP100		0.18

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: rs78025867;

hg19: chr3-18618853;