ENST00000670989.1:n.207-17137G>A

Variant names:

• chrX-141136709-C-T
• rs1016824
• ENST00000670989.1:n.207-17137G>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000670989.1(LDOC1):​n.207-17137G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.52 (10694 hom., 14895 hem., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: LDOC1 ENST00000670989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 1 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LDOC1	ENST00000670989.1		n.207-17137G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.517 AC: 54421 AN: 105186 Hom.: 10692 Cov.: 20

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.581

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.518

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.517 AC: 54422 AN: 105208 Hom.: 10694 Cov.: 20 AF XY: 0.528 AC XY: 14895 AN XY: 28228

African (AFR) AF: 0.355 AC: 10373 AN: 29253

American (AMR) AF: 0.478 AC: 4574 AN: 9571

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1406 AN: 2576

East Asian (EAS) AF: 0.407 AC: 1340 AN: 3290

South Asian (SAS) AF: 0.568 AC: 1330 AN: 2340

European-Finnish (FIN) AF: 0.640 AC: 2959 AN: 4623

Middle Eastern (MID) AF: 0.589 AC: 112 AN: 190

European-Non Finnish (NFE) AF: 0.612 AC: 31394 AN: 51308

Other (OTH) AF: 0.521 AC: 735 AN: 1412

Alfa AF: 0.560 Hom.: 49397

Bravo AF: 0.490

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.024
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1016824; hg19: chrX-140230896;