X-85095122-G-T

Position:

• chrX-85095122-G-T

Variant summary

Our verdict is Likely benign. Variant got -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

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 Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SATL1	NM_001367857.2	c.1694-126C>A		intron_variant		ENST00000644105.2	NP_001354786.1
SATL1	NM_001367858.2	c.1694-126C>A		intron_variant			NP_001354787.1
SATL1	NM_001012980.2	c.1694-126C>A		intron_variant			NP_001012998.2
SATL1	XM_047442081.1	c.1694-126C>A		intron_variant			XP_047298037.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SATL1	ENST00000644105.2	c.1694-126C>A		intron_variant			NM_001367857.2	ENSP00000494345.1

Frequencies

GnomAD3 genomes AF: 0.645 AC: 71272 AN: 110513 Hom.: 16175 Cov.: 22 AF XY: 0.653 AC XY: 21414 AN XY: 32799

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

Gnomad4 AFR exome AF: 0.535

Gnomad4 AMR exome AF: 0.675

Gnomad4 ASJ exome AF: 0.736

Gnomad4 EAS exome AF: 0.686

Gnomad4 SAS exome AF: 0.824

Gnomad4 FIN exome AF: 0.732

Gnomad4 NFE exome AF: 0.676

Gnomad4 OTH exome AF: 0.675

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

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.739

Gnomad4 EAS AF: 0.648

Gnomad4 SAS AF: 0.818

Gnomad4 FIN AF: 0.731

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.678

Alfa AF: 0.596 Hom.: 6097

Bravo AF: 0.634

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.65

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

Publications

LitVar

Other links and lift over

dbSNP: rs4828327; hg19: chrX-84350128;