rs12156848

Positions:

• chrX-141138057-G-A

Variant summary

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

The ENST00000670989.1(LDOC1):​n.207-18485C>T 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 0.118 in 112,121 control chromosomes in the GnomAD database, including 756 homozygotes. There are 3,919 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 0.12 (756 hom., 3919 hem., cov: 23)
• Consequence: LDOC1 ENST00000670989.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390

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=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LDOC1	ENST00000670989.1	n.207-18485C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.118 AC: 13235 AN: 112067 Hom.: 756 Cov.: 23 AF XY: 0.114 AC XY: 3916 AN XY: 34267

Gnomad AFR AF: 0.0224

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.0875

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.0877

Gnomad SAS AF: 0.0844

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.0795

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.0995

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

GnomAD4 genome AF: 0.118 AC: 13236 AN: 112121 Hom.: 756 Cov.: 23 AF XY: 0.114 AC XY: 3919 AN XY: 34331

Gnomad4 AFR AF: 0.0224

Gnomad4 AMR AF: 0.0877

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.0877

Gnomad4 SAS AF: 0.0847

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.0983

Alfa AF: 0.155 Hom.: 3543

Bravo AF: 0.110

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12156848; hg19: chrX-140232242;