10-96878324-T-C

Variant names:

• chr10-96878324-T-C
• rs4919058
• NM_001346516.2:c.-329-28941T>C

Variant summary

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

The ENST00000421806.4(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 ENST00000421806.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.871
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421806.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LCOR	NM_001346516.2	MANE Select	c.-329-28941T>C		intron	N/A	NP_001333445.1
	LCOR	NM_001170765.2		c.-329-28941T>C		intron	N/A	NP_001164236.1
	LCOR	NM_032440.4		c.-329-28941T>C		intron	N/A	NP_115816.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LCOR	ENST00000421806.4	TSL:3 MANE Select	c.-329-28941T>C		intron	N/A	ENSP00000490116.2
	LCOR	ENST00000371097.8	TSL:1	c.-329-28941T>C		intron	N/A	ENSP00000360138.3
	LCOR	ENST00000371103.8	TSL:1	c.-329-28941T>C		intron	N/A	ENSP00000360144.3

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

African (AFR) AF: 0.697 AC: 28883 AN: 41458

American (AMR) AF: 0.289 AC: 4401 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1033 AN: 3468

East Asian (EAS) AF: 0.475 AC: 2457 AN: 5174

South Asian (SAS) AF: 0.399 AC: 1925 AN: 4826

European-Finnish (FIN) AF: 0.164 AC: 1737 AN: 10564

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12253 AN: 67952

Other (OTH) AF: 0.345 AC: 731 AN: 2116

Alfa AF: 0.291 Hom.: 1616

Bravo AF: 0.375

Asia WGS AF: 0.515 AC: 1789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.38
PhyloP100		-0.87
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4919058; hg19: chr10-98638081;