rs10514670

Positions:

• chr3-18527800-G-C

Variant summary

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

The NR_125803.1(SATB1-AS1):​n.709+474G>C 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 0.0408 in 152,076 control chromosomes in the GnomAD database, including 165 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 0.041 (165 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SATB1-AS1 NR_125803.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SATB1-AS1	NR_125803.1	n.709+474G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SATB1-AS1	ENST00000683051.1	n.120+474G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0408 AC: 6205 AN: 151958 Hom.: 164 Cov.: 32

Gnomad AFR AF: 0.0109

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0448

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.0389

Gnomad SAS AF: 0.0231

Gnomad FIN AF: 0.0339

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0606

Gnomad OTH AF: 0.0321

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0408 AC: 6208 AN: 152076 Hom.: 165 Cov.: 32 AF XY: 0.0385 AC XY: 2860 AN XY: 74352

Gnomad4 AFR AF: 0.0109

Gnomad4 AMR AF: 0.0448

Gnomad4 ASJ AF: 0.0435

Gnomad4 EAS AF: 0.0390

Gnomad4 SAS AF: 0.0231

Gnomad4 FIN AF: 0.0339

Gnomad4 NFE AF: 0.0607

Gnomad4 OTH AF: 0.0318

Alfa AF: 0.0493 Hom.: 29

Bravo AF: 0.0403

Asia WGS AF: 0.0380 AC: 131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.51
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514670; hg19: chr3-18569292;