rs12156848

Variant names:

• chrX-141138057-G-A
• rs12156848
• ENST00000670989.1:n.207-18485C>T

Variant summary

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

The ENST00000670989.1(LDOC1):​n.207-18485C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• 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=-1.03).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LDOC1	ENST00000670989.1	n.207-18485C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.118 AC: 13235 AN: 112067 Hom.: 756 Cov.: 23

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

African (AFR) AF: 0.0224 AC: 694 AN: 31009

American (AMR) AF: 0.0877 AC: 928 AN: 10580

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 482 AN: 2651

East Asian (EAS) AF: 0.0877 AC: 309 AN: 3522

South Asian (SAS) AF: 0.0847 AC: 231 AN: 2728

European-Finnish (FIN) AF: 0.203 AC: 1228 AN: 6044

Middle Eastern (MID) AF: 0.0734 AC: 16 AN: 218

European-Non Finnish (NFE) AF: 0.167 AC: 8897 AN: 53178

Other (OTH) AF: 0.0983 AC: 150 AN: 1526

Alfa AF: 0.153 Hom.: 4474

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
PhyloP100		-0.039

Splicing

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

Other links and lift over

dbSNP: rs12156848; hg19: chrX-140232242;