chrX-141146369-G-A

Variant names:

• chrX-141146369-G-A
• rs7885649
• ENST00000670989.1:n.207-26797C>T

Variant summary

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

The ENST00000670989.1(LDOC1):​n.207-26797C>T 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 0.56 (12982 hom., 18699 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: LDOC1 ENST00000670989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52
• Publications: 3 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=-1.0).

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.207-26797C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.558 AC: 61908 AN: 110934 Hom.: 12979 Cov.: 23

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.600

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: 0.558 AC: 61922 AN: 110986 Hom.: 12982 Cov.: 23 AF XY: 0.563 AC XY: 18699 AN XY: 33232

African (AFR) AF: 0.311 AC: 9525 AN: 30596

American (AMR) AF: 0.704 AC: 7361 AN: 10458

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 1611 AN: 2630

East Asian (EAS) AF: 0.803 AC: 2804 AN: 3491

South Asian (SAS) AF: 0.589 AC: 1556 AN: 2642

European-Finnish (FIN) AF: 0.605 AC: 3558 AN: 5878

Middle Eastern (MID) AF: 0.674 AC: 147 AN: 218

European-Non Finnish (NFE) AF: 0.645 AC: 34136 AN: 52890

Other (OTH) AF: 0.606 AC: 920 AN: 1517

Alfa AF: 0.613 Hom.: 76280

Bravo AF: 0.561

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.054
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs7885649; hg19: chrX-140240569;