rs7885649

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).

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.207-26797C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7885649;

hg19: chrX-140240569;