X-85228329-T-C

Variant names:

• chrX-85228329-T-C
• rs2188734
• NM_001367857.2:c.-434-4003A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 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: Benign. The variant received -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 rank	MANE	Protein	UniProt
SATL1	NM_001367857.2	c.-434-4003A>G		intron_variant	Intron 1 of 7	ENST00000644105.2	NP_001354786.1
SATL1	NM_001367858.2	c.-895-4003A>G		intron_variant	Intron 1 of 11		NP_001354787.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SATL1	ENST00000644105.2	c.-434-4003A>G		intron_variant	Intron 1 of 7		NM_001367857.2	ENSP00000494345.1
SATL1	ENST00000646118.1	c.-1051-4003A>G		intron_variant	Intron 1 of 12			ENSP00000493598.1
SATL1	ENST00000646235.1	c.-895-4003A>G		intron_variant	Intron 1 of 11			ENSP00000495329.1
SATL1	ENST00000647304.1	n.284-4003A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.241 AC: 26509 AN: 109979 Hom.: 3390 Cov.: 21

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

African (AFR) AF: 0.490 AC: 14773 AN: 30138

American (AMR) AF: 0.168 AC: 1744 AN: 10400

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 472 AN: 2618

East Asian (EAS) AF: 0.156 AC: 543 AN: 3487

South Asian (SAS) AF: 0.209 AC: 541 AN: 2589

European-Finnish (FIN) AF: 0.152 AC: 891 AN: 5857

Middle Eastern (MID) AF: 0.144 AC: 31 AN: 215

European-Non Finnish (NFE) AF: 0.138 AC: 7228 AN: 52540

Other (OTH) AF: 0.200 AC: 300 AN: 1499

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
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs2188734; hg19: chrX-84483335;