3-18527800-G-C

Variant names:

• chr3-18527800-G-C
• rs10514670
• ENST00000598740.6:n.1041G>C

Variant summary

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

The ENST00000598740.6(SATB1-AS1):​n.1041G>C variant causes a non coding transcript exon 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 ENST00000598740.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 2 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=-0.89).
• 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 rank	MANE	Protein	UniProt
SATB1-AS1	NR_125803.1	n.709+474G>C		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SATB1-AS1	ENST00000598740.6	n.1041G>C		non_coding_transcript_exon_variant	Exon 6 of 6	5
SATB1-AS1	ENST00000627496.2	n.316G>C		non_coding_transcript_exon_variant	Exon 3 of 4	5
SATB1-AS1	ENST00000414198.7	n.922+474G>C		intron_variant	Intron 6 of 6	2

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.0109 AC: 453 AN: 41522

American (AMR) AF: 0.0448 AC: 684 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0435 AC: 151 AN: 3472

East Asian (EAS) AF: 0.0390 AC: 202 AN: 5178

South Asian (SAS) AF: 0.0231 AC: 111 AN: 4800

European-Finnish (FIN) AF: 0.0339 AC: 359 AN: 10596

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0607 AC: 4121 AN: 67938

Other (OTH) AF: 0.0318 AC: 67 AN: 2110

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
PhyloP100		-0.090

Splicing

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

Other links and lift over

dbSNP: rs10514670; hg19: chr3-18569292;