rs11064153

Variant names:

• chr12-6379284-T-C
• rs11064153
• NM_001270987.2:c.39+3690T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LTBR	NM_001270987.2	c.39+3690T>C		intron_variant	Intron 1 of 9		NP_001257916.1
LTBR	NM_001414309.1	c.39+3690T>C		intron_variant	Intron 1 of 9		NP_001401238.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LTBR	ENST00000539925.5	c.39+3690T>C		intron_variant	Intron 1 of 9	2		ENSP00000440875.1
LTBR	ENST00000542830.5	n.265+3690T>C		intron_variant	Intron 2 of 4	4
LTBR	ENST00000546296.5	n.550+3690T>C		intron_variant	Intron 1 of 2	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

African (AFR) AF: 0.411 AC: 17007 AN: 41424

American (AMR) AF: 0.412 AC: 6290 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 935 AN: 3468

East Asian (EAS) AF: 0.612 AC: 3152 AN: 5152

South Asian (SAS) AF: 0.358 AC: 1723 AN: 4816

European-Finnish (FIN) AF: 0.244 AC: 2583 AN: 10574

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14722 AN: 67968

Other (OTH) AF: 0.311 AC: 656 AN: 2106

Alfa AF: 0.262 Hom.: 16839

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
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11064153; hg19: chr12-6488450;