X-85095004-A-G

Variant names:

• chrX-85095004-A-G
• rs4828326
• NM_001367857.2:c.1694-8T>C

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_Strong BP6

The NM_001367857.2(SATL1):​c.1694-8T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.64 (15838 hom., 21055 hem., cov: 22)
  • Exomes 𝑓: 0.69 (152733 hom. 188388 hem.)
  • Failed GnomAD Quality Control
• Consequence: SATL1 NM_001367857.2 splice_region, intron
• Scores: Splicing: ADA: 0.0004465
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: 0.393
• Publications: 9 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]

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant X-85095004-A-G is Benign according to our data. Variant chrX-85095004-A-G is described in ClinVar as Benign. ClinVar VariationId is 3059185.Status of the report is no_assertion_criteria_provided, 0 stars.

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.1694-8T>C		splice_region intron	N/A	NP_001354786.1	Q86VE3-1
	SATL1	NM_001367858.2		c.1694-8T>C		splice_region intron	N/A	NP_001354787.1	A0A2R8YFQ0
	SATL1	NM_001012980.2		c.1694-8T>C		splice_region intron	N/A	NP_001012998.2	Q86VE3-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SATL1	ENST00000644105.2	MANE Select	c.1694-8T>C		splice_region intron	N/A	ENSP00000494345.1	Q86VE3-1
	SATL1	ENST00000509231.1	TSL:1	c.1694-8T>C		splice_region intron	N/A	ENSP00000425421.1	Q86VE3-2
	SATL1	ENST00000646118.1		c.1694-8T>C		splice_region intron	N/A	ENSP00000493598.1	Q86VE3-1

Frequencies

GnomAD3 genomes AF: 0.636 AC: 70235 AN: 110415 Hom.: 15847 Cov.: 22

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.662

GnomAD2 exomes AF: 0.682 AC: 108374 AN: 158818 AF XY: 0.701

Gnomad AFR exome AF: 0.503

Gnomad AMR exome AF: 0.664

Gnomad ASJ exome AF: 0.727

Gnomad EAS exome AF: 0.637

Gnomad FIN exome AF: 0.736

Gnomad NFE exome AF: 0.680

Gnomad OTH exome AF: 0.697

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.685 AC: 638444 AN: 931580 Hom.: 152733 Cov.: 16 AF XY: 0.711 AC XY: 188388 AN XY: 264848

African (AFR) AF: 0.509 AC: 11916 AN: 23402

American (AMR) AF: 0.673 AC: 22769 AN: 33855

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 13044 AN: 17845

East Asian (EAS) AF: 0.676 AC: 19813 AN: 29291

South Asian (SAS) AF: 0.815 AC: 39757 AN: 48769

European-Finnish (FIN) AF: 0.727 AC: 28633 AN: 39405

Middle Eastern (MID) AF: 0.728 AC: 2749 AN: 3774

European-Non Finnish (NFE) AF: 0.680 AC: 472584 AN: 694896

Other (OTH) AF: 0.674 AC: 27179 AN: 40343

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.636 AC: 70248 AN: 110468 Hom.: 15838 Cov.: 22 AF XY: 0.643 AC XY: 21055 AN XY: 32748

African (AFR) AF: 0.507 AC: 15427 AN: 30425

American (AMR) AF: 0.685 AC: 7106 AN: 10373

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 1944 AN: 2635

East Asian (EAS) AF: 0.643 AC: 2233 AN: 3472

South Asian (SAS) AF: 0.813 AC: 2088 AN: 2568

European-Finnish (FIN) AF: 0.729 AC: 4232 AN: 5806

Middle Eastern (MID) AF: 0.794 AC: 170 AN: 214

European-Non Finnish (NFE) AF: 0.675 AC: 35662 AN: 52800

Other (OTH) AF: 0.659 AC: 991 AN: 1503

Alfa AF: 0.664 Hom.: 8524

Bravo AF: 0.625

ClinVar

ClinVar submissions

Significance: Benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	SATL1-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.9
DANN	Benign	0.71
PhyloP100		0.39
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00045
dbscSNV1_RF	Benign	0.020
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4828326; hg19: chrX-84350010; COSMIC: COSV60576532; COSMIC: COSV60576532;