X-85212039-C-T

Variant names:

• chrX-85212039-C-T
• rs2285602
• NM_001367857.2:c.-313+12166G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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]

ENSG00000235461 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367857.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SATL1	NM_001367857.2	MANE Select	c.-313+12166G>A		intron	N/A	NP_001354786.1	Q86VE3-1
	SATL1	NM_001367858.2		c.-774+12166G>A		intron	N/A	NP_001354787.1	A0A2R8YFQ0
	LOC101928128	NR_110651.1		n.235C>T		non_coding_transcript_exon	Exon 2 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SATL1	ENST00000644105.2	MANE Select	c.-313+12166G>A		intron	N/A	ENSP00000494345.1	Q86VE3-1
	SATL1	ENST00000646118.1		c.-930+12166G>A		intron	N/A	ENSP00000493598.1	Q86VE3-1
	SATL1	ENST00000646235.1		c.-774+12166G>A		intron	N/A	ENSP00000495329.1	A0A2R8YFQ0

Frequencies

GnomAD3 genomes AF: 0.129 AC: 14309 AN: 110800 Hom.: 714 Cov.: 22

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

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) AC: 0 AN: 0

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

African (AFR) AF: 0.121 AC: 3717 AN: 30610

American (AMR) AF: 0.0878 AC: 913 AN: 10396

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 469 AN: 2629

East Asian (EAS) AF: 0.127 AC: 445 AN: 3496

South Asian (SAS) AF: 0.175 AC: 459 AN: 2627

European-Finnish (FIN) AF: 0.154 AC: 915 AN: 5935

Middle Eastern (MID) AF: 0.117 AC: 25 AN: 214

European-Non Finnish (NFE) AF: 0.136 AC: 7191 AN: 52751

Other (OTH) AF: 0.109 AC: 164 AN: 1509

Alfa AF: 0.136 Hom.: 3732

Bravo AF: 0.121

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.34
PhyloP100		0.53
Mutation Taster		=99/1	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2285602; hg19: chrX-84467045;