chr8-85110101-CT-C

Position:

• chr8-85110101-CT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_033402.5(LRRCC1):​c.311-3del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0479 in 770,880 control chromosomes in the GnomAD database, including 10 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0039 (2 hom., cov: 33)
  • Exomes 𝑓: 0.058 (8 hom.)
• Consequence: LRRCC1 NM_033402.5 splice_polypyrimidine_tract, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.363

Genes affected

LRRCC1 (HGNC:29373): (leucine rich repeat and coiled-coil centrosomal protein 1) This gene encodes a centrosomal protein that maintains the structural integrity of the centrosome and plays a key role in mitotic spindle formation. The encoded protein contains an N-terminal leucine-rich repeat domain and a C-terminal coiled-coil domain. It associates with the centrosome throughout the cell cycle and accumulates on the mitotic centrosome. [provided by RefSeq, Mar 2017]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 8-85110101-CT-C is Benign according to our data. Variant chr8-85110101-CT-C is described in ClinVar as [Benign]. Clinvar id is 1669647.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRRCC1	NM_033402.5	c.311-3del		splice_polypyrimidine_tract_variant, intron_variant		ENST00000360375.8	NP_208325.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRRCC1	ENST00000360375.8	c.311-3del		splice_polypyrimidine_tract_variant, intron_variant		1	NM_033402.5	ENSP00000353538	P2

Frequencies

GnomAD3 genomes AF: 0.00390 AC: 567 AN: 145240 Hom.: 2 Cov.: 33

Gnomad AFR AF: 0.00175

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00646

Gnomad ASJ AF: 0.00207

Gnomad EAS AF: 0.000399

Gnomad SAS AF: 0.000863

Gnomad FIN AF: 0.00336

Gnomad MID AF: 0.00662

Gnomad NFE AF: 0.00521

Gnomad OTH AF: 0.00816

GnomAD3 exomes AF: 0.0910 AC: 6071 AN: 66706 Hom.: 1 AF XY: 0.0944 AC XY: 3414 AN XY: 36166

Gnomad AFR exome AF: 0.0617

Gnomad AMR exome AF: 0.102

Gnomad ASJ exome AF: 0.127

Gnomad EAS exome AF: 0.0805

Gnomad SAS exome AF: 0.112

Gnomad FIN exome AF: 0.0839

Gnomad NFE exome AF: 0.0884

Gnomad OTH exome AF: 0.120

GnomAD4 exome AF: 0.0581 AC: 36374 AN: 625584 Hom.: 8 Cov.: 8 AF XY: 0.0584 AC XY: 18793 AN XY: 321566

Gnomad4 AFR exome AF: 0.0537

Gnomad4 AMR exome AF: 0.0555

Gnomad4 ASJ exome AF: 0.0589

Gnomad4 EAS exome AF: 0.0482

Gnomad4 SAS exome AF: 0.0672

Gnomad4 FIN exome AF: 0.0537

Gnomad4 NFE exome AF: 0.0583

Gnomad4 OTH exome AF: 0.0600

GnomAD4 genome AF: 0.00391 AC: 568 AN: 145296 Hom.: 2 Cov.: 33 AF XY: 0.00370 AC XY: 261 AN XY: 70632

Gnomad4 AFR AF: 0.00175

Gnomad4 AMR AF: 0.00652

Gnomad4 ASJ AF: 0.00207

Gnomad4 EAS AF: 0.000400

Gnomad4 SAS AF: 0.000867

Gnomad4 FIN AF: 0.00336

Gnomad4 NFE AF: 0.00521

Gnomad4 OTH AF: 0.00810

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jul 10, 2023

- -

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs755909227; hg19: chr8-86022336;