X-85095122-G-T

Variant names:

• chrX-85095122-G-T
• rs4828327
• NM_001367857.2:c.1694-126C>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001367857.2(SATL1):​c.1694-126C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.64 (16167 hom., 21444 hem., cov: 22)
  • Exomes 𝑓: 0.69 (56517 hom. 73224 hem.)
  • Failed GnomAD Quality Control
• Consequence: SATL1 NM_001367857.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.468
• Publications: 3 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 -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SATL1	NM_001367857.2	MANE Select	c.1694-126C>A		intron	N/A	NP_001354786.1
	SATL1	NM_001367858.2		c.1694-126C>A		intron	N/A	NP_001354787.1
	SATL1	NM_001012980.2		c.1694-126C>A		intron	N/A	NP_001012998.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SATL1	ENST00000644105.2	MANE Select	c.1694-126C>A		intron	N/A	ENSP00000494345.1
	SATL1	ENST00000509231.1	TSL:1	c.1694-126C>A		intron	N/A	ENSP00000425421.1
	SATL1	ENST00000646118.1		c.1694-126C>A		intron	N/A	ENSP00000493598.1

Frequencies

GnomAD3 genomes AF: 0.645 AC: 71272 AN: 110513 Hom.: 16175 Cov.: 22

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.681

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.689 AC: 237458 AN: 344629 Hom.: 56517 AF XY: 0.708 AC XY: 73224 AN XY: 103385

African (AFR) AF: 0.535 AC: 5843 AN: 10917

American (AMR) AF: 0.675 AC: 12983 AN: 19222

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 7859 AN: 10684

East Asian (EAS) AF: 0.686 AC: 15865 AN: 23129

South Asian (SAS) AF: 0.824 AC: 18934 AN: 22981

European-Finnish (FIN) AF: 0.732 AC: 22813 AN: 31180

Middle Eastern (MID) AF: 0.728 AC: 1827 AN: 2511

European-Non Finnish (NFE) AF: 0.676 AC: 138214 AN: 204567

Other (OTH) AF: 0.675 AC: 13120 AN: 19438

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.645 AC: 71289 AN: 110564 Hom.: 16167 Cov.: 22 AF XY: 0.653 AC XY: 21444 AN XY: 32860

African (AFR) AF: 0.536 AC: 16284 AN: 30405

American (AMR) AF: 0.689 AC: 7163 AN: 10391

Ashkenazi Jewish (ASJ) AF: 0.739 AC: 1952 AN: 2643

East Asian (EAS) AF: 0.648 AC: 2244 AN: 3465

South Asian (SAS) AF: 0.818 AC: 2134 AN: 2610

European-Finnish (FIN) AF: 0.731 AC: 4323 AN: 5910

Middle Eastern (MID) AF: 0.802 AC: 170 AN: 212

European-Non Finnish (NFE) AF: 0.675 AC: 35606 AN: 52751

Other (OTH) AF: 0.678 AC: 1015 AN: 1498

Alfa AF: 0.596 Hom.: 6097

Bravo AF: 0.634

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.65
PhyloP100		0.47
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs4828327; hg19: chrX-84350128;