1-110952011-C-CCATT

Position:

• chr1-110952011-C-CCATT

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP5

The NM_018372.4(LRIF1):​c.872_873insAATG​(p.Trp291Ter) variant causes a stop gained, frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: LRIF1 NM_018372.4 stop_gained, frameshift
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 2.07

Genes affected

LRIF1 (HGNC:30299): (ligand dependent nuclear receptor interacting factor 1) Predicted to enable retinoic acid receptor binding activity. Involved in dosage compensation by inactivation of X chromosome. Located in Barr body; centriolar satellite; and nucleoplasm. Colocalizes with chromosome, telomeric region. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 1-110952011-C-CCATT is Pathogenic according to our data. Variant chr1-110952011-C-CCATT is described in ClinVar as [Pathogenic]. Clinvar id is 1202610.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRIF1	NM_018372.4	c.872_873insAATG	p.Trp291Ter	stop_gained, frameshift_variant	2/4	ENST00000369763.5
LRIF1	XM_005271029.5	c.872_873insAATG	p.Trp291Ter	stop_gained, frameshift_variant	2/4
LRIF1	XM_017001769.3	c.872_873insAATG	p.Trp291Ter	stop_gained, frameshift_variant	2/4
LRIF1	NM_001006945.2	c.-12-1889_-12-1888insAATG		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRIF1	ENST00000369763.5	c.872_873insAATG	p.Trp291Ter	stop_gained, frameshift_variant	2/4	5	NM_018372.4	P1
	ENST00000440689.1	n.1695-172_1695-169dup		intron_variant, non_coding_transcript_variant		2
LRIF1	ENST00000485275.2	c.-12-1889_-12-1888insAATG		intron_variant		2
LRIF1	ENST00000494675.5	c.-13+520_-13+521insAATG		intron_variant		2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Facioscapulohumeral muscular dystrophy 3, digenic Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Aug 16, 2021

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-111494633;