rs7428395

Variant names:

• chr3-18778501-C-G
• rs7428395
• ENST00000425799.7:n.360+14710C>G

Your query was ambiguous. Multiple possible variants found:

• chr3-18778501-C-G
• chr3-18778501-C-T

Variant summary

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

The ENST00000425799.7(SATB1-AS1):​n.360+14710C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 151,908 control chromosomes in the GnomAD database, including 2,193 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 0.16 (2193 hom., cov: 32)
• Consequence: SATB1-AS1 ENST00000425799.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152
• Publications: 4 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.224 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	ENST00000425799.7	n.360+14710C>G		intron_variant	Intron 5 of 8	5
SATB1-AS1	ENST00000626982.2	n.351+14710C>G		intron_variant	Intron 4 of 4	5
SATB1-AS1	ENST00000630271.2	n.324+14710C>G		intron_variant	Intron 4 of 7	5

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23724 AN: 151790 Hom.: 2191 Cov.: 32

Gnomad AFR AF: 0.0679

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.0917

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.156 AC: 23736 AN: 151908 Hom.: 2193 Cov.: 32 AF XY: 0.158 AC XY: 11765 AN XY: 74246

African (AFR) AF: 0.0679 AC: 2818 AN: 41486

American (AMR) AF: 0.231 AC: 3511 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 554 AN: 3466

East Asian (EAS) AF: 0.0921 AC: 473 AN: 5134

South Asian (SAS) AF: 0.176 AC: 849 AN: 4812

European-Finnish (FIN) AF: 0.190 AC: 2007 AN: 10588

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.189 AC: 12860 AN: 67904

Other (OTH) AF: 0.175 AC: 368 AN: 2106

Alfa AF: 0.168 Hom.: 284

Bravo AF: 0.158

Asia WGS AF: 0.109 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.7
DANN	Benign	0.70
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs7428395; hg19: chr3-18819993;