rs7880499

Variant names:

• chrX-141136365-G-A
• rs7880499
• ENST00000670989.1:n.207-16793C>T

Your query was ambiguous. Multiple possible variants found:

• chrX-141136365-G-A
• chrX-141136365-G-C
• chrX-141136365-G-T

Variant summary

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

The ENST00000670989.1(LDOC1):​n.207-16793C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 110,821 control chromosomes in the GnomAD database, including 3,421 homozygotes. There are 9,161 hemizygotes in GnomAD. 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 0.28 (3421 hom., 9161 hem., cov: 23)
• Consequence: LDOC1 ENST00000670989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

Genes affected

LDOC1 (HGNC:6548): (LDOC1 regulator of NFKB signaling) The protein encoded by this gene contains a leucine zipper-like motif and a proline-rich region that shares marked similarity with an SH3-binding domain. The protein localizes to the nucleus and is down-regulated in some cancer cell lines. It is thought to regulate the transcriptional response mediated by the nuclear factor kappa B (NF-kappaB). The gene has been proposed as a tumor suppressor gene whose protein product may have an important role in the development and/or progression of some cancers. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LDOC1	ENST00000670989.1	n.207-16793C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.282 AC: 31241 AN: 110765 Hom.: 3419 Cov.: 23 AF XY: 0.277 AC XY: 9144 AN XY: 33027

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.282 AC: 31251 AN: 110821 Hom.: 3421 Cov.: 23 AF XY: 0.277 AC XY: 9161 AN XY: 33093

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.309

Alfa AF: 0.159 Hom.: 1199

Bravo AF: 0.307

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.6
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7880499; hg19: chrX-140230552;