13-42599062-T-C

Variant names:

• chr13-42599062-T-C
• rs3742257
• NM_003701.4:c.388-1690T>C

Variant summary

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

The NM_003701.4(TNFSF11):​c.388-1690T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,934 control chromosomes in the GnomAD database, including 19,460 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 0.50 (19460 hom., cov: 31)
• Consequence: TNFSF11 NM_003701.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 22 publications found

Genes affected

TNFSF11 (HGNC:11926): (TNF superfamily member 11) This gene encodes a member of the tumor necrosis factor (TNF) cytokine family which is a ligand for osteoprotegerin and functions as a key factor for osteoclast differentiation and activation. This protein was shown to be a dentritic cell survival factor and is involved in the regulation of T cell-dependent immune response. T cell activation was reported to induce expression of this gene and lead to an increase of osteoclastogenesis and bone loss. This protein was shown to activate antiapoptotic kinase AKT/PKB through a signaling complex involving SRC kinase and tumor necrosis factor receptor-associated factor (TRAF) 6, which indicated this protein may have a role in the regulation of cell apoptosis. Targeted disruption of the related gene in mice led to severe osteopetrosis and a lack of osteoclasts. The deficient mice exhibited defects in early differentiation of T and B lymphocytes, and failed to form lobulo-alveolar mammary structures during pregnancy. Two alternatively spliced transcript variants have been found. [provided by RefSeq, Jul 2008]

TNFSF11 Gene-Disease associations (from GenCC):

• autosomal recessive osteopetrosis 2

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
• autosomal recessive osteopetrosis

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNFSF11	NM_003701.4	c.388-1690T>C		intron_variant	Intron 2 of 4	ENST00000398795.7	NP_003692.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNFSF11	ENST00000398795.7	c.388-1690T>C		intron_variant	Intron 2 of 4	1	NM_003701.4	ENSP00000381775.3
TNFSF11	ENST00000358545.6	c.169-1690T>C		intron_variant	Intron 4 of 6	1		ENSP00000351347.2

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76366 AN: 151816 Hom.: 19441 Cov.: 31

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.503 AC: 76422 AN: 151934 Hom.: 19460 Cov.: 31 AF XY: 0.501 AC XY: 37209 AN XY: 74238

African (AFR) AF: 0.529 AC: 21910 AN: 41440

American (AMR) AF: 0.559 AC: 8536 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2330 AN: 3470

East Asian (EAS) AF: 0.512 AC: 2643 AN: 5164

South Asian (SAS) AF: 0.571 AC: 2755 AN: 4824

European-Finnish (FIN) AF: 0.405 AC: 4261 AN: 10528

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32225 AN: 67920

Other (OTH) AF: 0.525 AC: 1109 AN: 2112

Alfa AF: 0.490 Hom.: 77981

Bravo AF: 0.517

Asia WGS AF: 0.549 AC: 1907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.61
DANN	Benign	0.55
PhyloP100		0.0
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: rs3742257; hg19: chr13-43173198;