X-141130602-A-C

Variant names:

• chrX-141130602-A-C
• rs5907823
• ENST00000670989.1:n.207-11030T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000670989.1(LDOC1):​n.207-11030T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 108,081 control chromosomes in the GnomAD database, including 4,836 homozygotes. There are 10,150 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 0.33 (4836 hom., 10150 hem., cov: 22)
• Consequence: LDOC1 ENST00000670989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• 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=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.412 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

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.207-11030T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.329 AC: 35569 AN: 108034 Hom.: 4831 Cov.: 22

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.412

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.329 AC: 35591 AN: 108081 Hom.: 4836 Cov.: 22 AF XY: 0.329 AC XY: 10150 AN XY: 30829

African (AFR) AF: 0.153 AC: 4468 AN: 29117

American (AMR) AF: 0.342 AC: 3460 AN: 10128

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 996 AN: 2597

East Asian (EAS) AF: 0.337 AC: 1140 AN: 3379

South Asian (SAS) AF: 0.228 AC: 581 AN: 2551

European-Finnish (FIN) AF: 0.426 AC: 2380 AN: 5582

Middle Eastern (MID) AF: 0.425 AC: 88 AN: 207

European-Non Finnish (NFE) AF: 0.417 AC: 21838 AN: 52378

Other (OTH) AF: 0.335 AC: 493 AN: 1473

Alfa AF: 0.360 Hom.: 2371

Bravo AF: 0.314

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	4.5
PhyloP100		1.1

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: rs5907823;

hg19: chrX-140224790;