10-96878324-T-C

Position:

• chr10-96878324-T-C

Variant summary

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

The NM_001346516.2(LCOR):​c.-329-28941T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 152,012 control chromosomes in the GnomAD database, including 13,408 homozygotes. 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 0.35 (13408 hom., cov: 31)
• Consequence: LCOR NM_001346516.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.871

Genes affected

LCOR (HGNC:29503): (ligand dependent nuclear receptor corepressor) LCOR is a transcriptional corepressor widely expressed in fetal and adult tissues that is recruited to agonist-bound nuclear receptors through a single LxxLL motif, also referred to as a nuclear receptor (NR) box (Fernandes et al., 2003 [PubMed 12535528]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LCOR	NM_001346516.2	c.-329-28941T>C		intron_variant		ENST00000421806.4	NP_001333445.1
LCOR	NM_001170765.2	c.-329-28941T>C		intron_variant			NP_001164236.1
LCOR	NM_001170766.2	c.-329-28941T>C		intron_variant			NP_001164237.1
LCOR	NM_032440.4	c.-329-28941T>C		intron_variant			NP_115816.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LCOR	ENST00000421806.4	c.-329-28941T>C		intron_variant		3	NM_001346516.2	ENSP00000490116

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53548 AN: 151894 Hom.: 13363 Cov.: 31

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.353 AC: 53645 AN: 152012 Hom.: 13408 Cov.: 31 AF XY: 0.351 AC XY: 26121 AN XY: 74326

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.345

Alfa AF: 0.278 Hom.: 1436

Bravo AF: 0.375

Asia WGS AF: 0.515 AC: 1789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.38

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4919058; hg19: chr10-98638081;