15-58925895-C-T

Variant names:

• chr15-58925895-C-T
• rs4775101
• NM_024755.4:c.250+6461G>A

Variant summary

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

The NM_024755.4(SLTM):​c.250+6461G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 151,962 control chromosomes in the GnomAD database, including 32,167 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 0.63 (32167 hom., cov: 32)
• Consequence: SLTM NM_024755.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545
• Publications: 5 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLTM	NM_024755.4	c.250+6461G>A		intron_variant	Intron 2 of 20	ENST00000380516.7	NP_079031.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLTM	ENST00000380516.7	c.250+6461G>A		intron_variant	Intron 2 of 20	1	NM_024755.4	ENSP00000369887.2

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96181 AN: 151844 Hom.: 32174 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.633 AC: 96189 AN: 151962 Hom.: 32167 Cov.: 32 AF XY: 0.627 AC XY: 46572 AN XY: 74280

African (AFR) AF: 0.405 AC: 16751 AN: 41400

American (AMR) AF: 0.705 AC: 10771 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 2706 AN: 3466

East Asian (EAS) AF: 0.578 AC: 2987 AN: 5168

South Asian (SAS) AF: 0.514 AC: 2472 AN: 4812

European-Finnish (FIN) AF: 0.610 AC: 6424 AN: 10534

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.758 AC: 51555 AN: 67994

Other (OTH) AF: 0.715 AC: 1505 AN: 2106

Alfa AF: 0.719 Hom.: 144051

Bravo AF: 0.632

Asia WGS AF: 0.550 AC: 1915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.48
DANN	Benign	0.78
PhyloP100		-0.55
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: rs4775101; hg19: chr15-59218094;