chr10-96880089-G-A

Variant names:

• chr10-96880089-G-A
• rs17112190
• NM_001346516.2:c.-329-27176G>A

Variant summary

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

The NM_001346516.2(LCOR):​c.-329-27176G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,204 control chromosomes in the GnomAD database, including 2,243 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 0.14 (2243 hom., cov: 33)
• Consequence: LCOR NM_001346516.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 12 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LCOR	NM_001346516.2	c.-329-27176G>A		intron_variant	Intron 2 of 7	ENST00000421806.4	NP_001333445.1
LCOR	NM_001170765.2	c.-329-27176G>A		intron_variant	Intron 2 of 7		NP_001164236.1
LCOR	NM_032440.4	c.-329-27176G>A		intron_variant	Intron 2 of 7		NP_115816.2
LCOR	NM_001170766.2	c.-329-27176G>A		intron_variant	Intron 2 of 8		NP_001164237.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LCOR	ENST00000421806.4	c.-329-27176G>A		intron_variant	Intron 2 of 7	3	NM_001346516.2	ENSP00000490116.2

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22026 AN: 152086 Hom.: 2240 Cov.: 33

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0987

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.0102

Gnomad SAS AF: 0.0308

Gnomad FIN AF: 0.0817

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.145 AC: 22055 AN: 152204 Hom.: 2243 Cov.: 33 AF XY: 0.139 AC XY: 10349 AN XY: 74384

African (AFR) AF: 0.283 AC: 11746 AN: 41518

American (AMR) AF: 0.0984 AC: 1504 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 485 AN: 3472

East Asian (EAS) AF: 0.0102 AC: 53 AN: 5182

South Asian (SAS) AF: 0.0304 AC: 147 AN: 4828

European-Finnish (FIN) AF: 0.0817 AC: 865 AN: 10588

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6884 AN: 68010

Other (OTH) AF: 0.123 AC: 261 AN: 2114

Alfa AF: 0.120 Hom.: 3943

Bravo AF: 0.151

Asia WGS AF: 0.0420 AC: 147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.34
PhyloP100		-0.12
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs17112190; hg19: chr10-98639846;