15-58919912-G-A

Variant names:

• chr15-58919912-G-A
• rs3145
• NM_024755.4:c.251-2913C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024755.4(SLTM):​c.251-2913C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 152,048 control chromosomes in the GnomAD database, including 32,879 homozygotes. 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 (32879 hom., cov: 31)
• Consequence: SLTM NM_024755.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.670
• Publications: 3 publications found

Genes affected

SLTM (HGNC:20709): (SAFB like transcription modulator) Enables RNA binding activity. Predicted to be involved in regulation of mRNA processing and regulation of transcription by RNA polymerase II. Located in nuclear body. [provided by Alliance of Genome Resources, Apr 2022]

RNF111 (HGNC:17384): (ring finger protein 111) The protein encoded by this gene is a nuclear RING-domain containing E3 ubiquitin ligase. This protein interacts with the transforming growth factor (TGF) -beta/NODAL signaling pathway by promoting the ubiquitination and proteosomal degradation of negative regulators, like SMAD proteins, and thereby enhances TGF-beta target-gene transcription. As a modulator of the nodal signaling cascade, this gene plays a critical role in the induction of mesoderm during embryonic development. Alternative splicing of this gene results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024755.4. 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
	SLTM	NM_024755.4	MANE Select	c.251-2913C>T		intron	N/A	NP_079031.2
	SLTM	NM_001013843.3		c.251-2913C>T		intron	N/A	NP_001013865.1
	SLTM	NR_135042.2		n.365-2913C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLTM	ENST00000380516.7	TSL:1 MANE Select	c.251-2913C>T		intron	N/A	ENSP00000369887.2
	SLTM	ENST00000249736.11	TSL:5	c.251-2913C>T		intron	N/A	ENSP00000249736.7
	SLTM	ENST00000559880.5	TSL:3	c.251-2913C>T		intron	N/A	ENSP00000453065.1

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97013 AN: 151930 Hom.: 32887 Cov.: 31

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.719

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.638 AC: 97020 AN: 152048 Hom.: 32879 Cov.: 31 AF XY: 0.632 AC XY: 46987 AN XY: 74318

African (AFR) AF: 0.399 AC: 16551 AN: 41436

American (AMR) AF: 0.712 AC: 10894 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2711 AN: 3466

East Asian (EAS) AF: 0.579 AC: 2992 AN: 5172

South Asian (SAS) AF: 0.524 AC: 2522 AN: 4816

European-Finnish (FIN) AF: 0.615 AC: 6491 AN: 10554

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.769 AC: 52262 AN: 67994

Other (OTH) AF: 0.720 AC: 1522 AN: 2114

Alfa AF: 0.727 Hom.: 20785

Bravo AF: 0.637

Asia WGS AF: 0.554 AC: 1931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.58
PhyloP100		0.67
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: rs3145; hg19: chr15-59212111;