rs2188734

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.647
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE UniProt
SATL1NM_001367857.2 linkuse as main transcriptc.-434-4003A>G intron_variant ENST00000644105.2
SATL1NM_001367858.2 linkuse as main transcriptc.-895-4003A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SATL1ENST00000644105.2 linkuse as main transcriptc.-434-4003A>G intron_variant NM_001367857.2 A2Q86VE3-1
SATL1ENST00000646118.1 linkuse as main transcriptc.-1051-4003A>G intron_variant A2Q86VE3-1
SATL1ENST00000646235.1 linkuse as main transcriptc.-895-4003A>G intron_variant
SATL1ENST00000647304.1 linkuse as main transcriptn.284-4003A>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.241
AC:
26509
AN:
109979
Hom.:
3390
Cov.:
21
AF XY:
0.225
AC XY:
7290
AN XY:
32349
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.490
Gnomad4 AMR
AF:
0.168
Gnomad4 ASJ
AF:
0.180
Gnomad4 EAS
AF:
0.156
Gnomad4 SAS
AF:
0.209
Gnomad4 FIN
AF:
0.152
Gnomad4 NFE
AF:
0.138
Gnomad4 OTH
AF:
0.200
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

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2188734; hg19: chrX-84483335; API