rs2188734

chrX-85228329-T-CchrX-85228329-T-G

Variant summary

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

The NM_001367857.2(SATL1):c.-434-4003A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 110,028 control chromosomes in the GnomAD database, including 3,388 homozygotes. There are 7,327 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 0.24 (3388 hom., 7327 hem., cov: 21)
• Consequence: SATL1 NM_001367857.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SATL1	NM_001367857.2	c.-434-4003A>G		intron_variant		ENST00000644105.2
SATL1	NM_001367858.2	c.-895-4003A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SATL1	ENST00000644105.2	c.-434-4003A>G		intron_variant			NM_001367857.2	A2
SATL1	ENST00000646118.1	c.-1051-4003A>G		intron_variant				A2
SATL1	ENST00000646235.1	c.-895-4003A>G		intron_variant
SATL1	ENST00000647304.1	n.284-4003A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.241 AC: 26509 AN: 109979 Hom.: 3390 Cov.: 21 AF XY: 0.225 AC XY: 7290 AN XY: 32349

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.0423

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.241 AC: 26552 AN: 110028 Hom.: 3388 Cov.: 21 AF XY: 0.226 AC XY: 7327 AN XY: 32408

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.200

Alfa AF: 0.189 Hom.: 1111

Bravo AF: 0.249

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.084
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2188734; hg19: chrX-84483335;