chr3-18577361-A-T

Variant names:

• chr3-18577361-A-T
• rs78025867
• ENST00000456253.6:n.610-8026A>T

Variant summary

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

The ENST00000456253.6(SATB1-AS1):​n.610-8026A>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 ENST00000456253.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.155 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	ENST00000456253.6	n.610-8026A>T		intron_variant	Intron 5 of 6	5
SATB1-AS1	ENST00000595250.5	n.462-8259A>T		intron_variant	Intron 4 of 4	5
SATB1-AS1	ENST00000595388.5	n.364+50035A>T		intron_variant	Intron 3 of 4	5

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

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.0311

Gnomad4 ASJ AF: 0.00807

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00145

Gnomad4 FIN AF: 0.000188

Gnomad4 NFE AF: 0.00357

Gnomad4 OTH AF: 0.0491

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.0
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs78025867; hg19: chr3-18618853;