rs11064153

Positions:

• chr12-6379284-T-C
• chr12-6379284-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001270987.2(LTBR):​c.39+3690T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 151,962 control chromosomes in the GnomAD database, including 8,273 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 0.31 (8273 hom., cov: 32)
• Consequence: LTBR NM_001270987.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

Genes affected

LTBR (HGNC:6718): (lymphotoxin beta receptor) This gene encodes a member of the tumor necrosis factor receptor superfamily. The major ligands of this receptor include lymphotoxin alpha/beta and tumor necrosis factor ligand superfamily member 14. The encoded protein plays a role in signalling during the development of lymphoid and other organs, lipid metabolism, immune response, and programmed cell death. Activity of this receptor has also been linked to carcinogenesis. Alternatively spliced transcript variants encoding multiple isoforms have been observed. [provided by RefSeq, Aug 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LTBR	NM_001270987.2	c.39+3690T>C		intron_variant			NP_001257916.1
LTBR	NM_001414309.1	c.39+3690T>C		intron_variant			NP_001401238.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LTBR	ENST00000539925.5	c.39+3690T>C		intron_variant		2		ENSP00000440875	A2
LTBR	ENST00000542830.5	n.265+3690T>C		intron_variant, non_coding_transcript_variant		4
LTBR	ENST00000546296.5	n.550+3690T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47228 AN: 151842 Hom.: 8257 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.311 AC: 47277 AN: 151962 Hom.: 8273 Cov.: 32 AF XY: 0.318 AC XY: 23623 AN XY: 74266

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.612

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.311

Alfa AF: 0.250 Hom.: 5554

Bravo AF: 0.328

Asia WGS AF: 0.488 AC: 1694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11064153; hg19: chr12-6488450;