rs5907823

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.08
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

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
LDOC1ENST00000670989.1 linkuse as main transcriptn.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
show subpopulations
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
show subpopulations
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs5907823; hg19: chrX-140224790; API