rs17069906

chr18-62381161-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_003839.4(TNFRSF11A):c.1568-3590A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.02 in 152,288 control chromosomes in the GnomAD database, including 47 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 0.020 (47 hom., cov: 31)
• Consequence: TNFRSF11A NM_003839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760

Genes affected

TNFRSF11A (HGNC:11908): (TNF receptor superfamily member 11a) The protein encoded by this gene is a member of the TNF-receptor superfamily. This receptors can interact with various TRAF family proteins, through which this receptor induces the activation of NF-kappa B and MAPK8/JNK. This receptor and its ligand are important regulators of the interaction between T cells and dendritic cells. This receptor is also an essential mediator for osteoclast and lymph node development. Mutations at this locus have been associated with familial expansile osteolysis, autosomal recessive osteopetrosis, and Paget disease of bone. Alternatively spliced transcript variants have been described for this locus. [provided by RefSeq, Aug 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.02 (3047/152288) while in subpopulation NFE AF= 0.0283 (1922/68024). AF 95% confidence interval is 0.0272. There are 47 homozygotes in gnomad4. There are 1502 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 47 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNFRSF11A	NM_003839.4	c.1568-3590A>G		intron_variant		ENST00000586569.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNFRSF11A	ENST00000586569.3	c.1568-3590A>G		intron_variant		1	NM_003839.4	P2
TNFRSF11A	ENST00000269485.11	c.617-3590A>G		intron_variant		1		A2

Frequencies

GnomAD3 genomes AF: 0.0200 AC: 3049 AN: 152170 Hom.: 47 Cov.: 31

Gnomad AFR AF: 0.00502

Gnomad AMI AF: 0.0604

Gnomad AMR AF: 0.0149

Gnomad ASJ AF: 0.0124

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0108

Gnomad FIN AF: 0.0464

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0283

Gnomad OTH AF: 0.0215

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

GnomAD4 genome AF: 0.0200 AC: 3047 AN: 152288 Hom.: 47 Cov.: 31 AF XY: 0.0202 AC XY: 1502 AN XY: 74456

Gnomad4 AFR AF: 0.00500

Gnomad4 AMR AF: 0.0148

Gnomad4 ASJ AF: 0.0124

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0108

Gnomad4 FIN AF: 0.0464

Gnomad4 NFE AF: 0.0283

Gnomad4 OTH AF: 0.0208

Alfa AF: 0.0239 Hom.: 8

Bravo AF: 0.0174

Asia WGS AF: 0.00462 AC: 16 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.3
Dann	Benign	0.39

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

Publications

LitVar

Other links and lift over

dbSNP: rs17069906; hg19: chr18-60048394;