X-141136365-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000670989.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LDOC1	ENST00000670989.1		n.207-16793C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.282 AC: 31241 AN: 110765 Hom.: 3419 Cov.: 23

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

African (AFR) AF: 0.355 AC: 10810 AN: 30470

American (AMR) AF: 0.388 AC: 4010 AN: 10331

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 645 AN: 2635

East Asian (EAS) AF: 0.498 AC: 1733 AN: 3482

South Asian (SAS) AF: 0.334 AC: 893 AN: 2672

European-Finnish (FIN) AF: 0.158 AC: 937 AN: 5915

Middle Eastern (MID) AF: 0.329 AC: 69 AN: 210

European-Non Finnish (NFE) AF: 0.218 AC: 11525 AN: 52922

Other (OTH) AF: 0.309 AC: 469 AN: 1517

Alfa AF: 0.159 Hom.: 1199

Bravo AF: 0.307

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.6
DANN	Benign	0.69
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs7880499; hg19: chrX-140230552;