X-141130602-A-C

Position:

• chrX-141130602-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000670989.1(LDOC1):​n.207-11030T>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LDOC1	ENST00000670989.1	n.207-11030T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.329 AC: 35569 AN: 108034 Hom.: 4831 Cov.: 22 AF XY: 0.329 AC XY: 10133 AN XY: 30772

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

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.335

Alfa AF: 0.360 Hom.: 2371

Bravo AF: 0.314

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5907823; hg19: chrX-140224790;