rs2285602

chrX-85212039-C-T

Variant summary

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

The NM_001367857.2(SATL1):c.-313+12166G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 110,851 control chromosomes in the GnomAD database, including 714 homozygotes. There are 4,032 hemizygotes in GnomAD. 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 0.13 (714 hom., 4032 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: SATL1 NM_001367857.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529

Genes affected

SATL1 (HGNC:27992): (spermidine/spermine N1-acetyl transferase like 1) Predicted to enable N-acetyltransferase activity. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SATL1	NM_001367857.2	c.-313+12166G>A		intron_variant		ENST00000644105.2
LOC101928128	NR_110651.1	n.235C>T		non_coding_transcript_exon_variant	2/4
SATL1	NM_001367858.2	c.-774+12166G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SATL1	ENST00000644105.2	c.-313+12166G>A		intron_variant			NM_001367857.2	A2
	ENST00000669792.1	n.203C>T		non_coding_transcript_exon_variant	2/5

Frequencies

GnomAD3 genomes AF: 0.129 AC: 14309 AN: 110800 Hom.: 714 Cov.: 22 AF XY: 0.122 AC XY: 4019 AN XY: 33068

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0875

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.106

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.129 AC: 14325 AN: 110851 Hom.: 714 Cov.: 22 AF XY: 0.122 AC XY: 4032 AN XY: 33129

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.0878

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.109

Alfa AF: 0.140 Hom.: 2554

Bravo AF: 0.121

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.7
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2285602; hg19: chrX-84467045;