1-110917225-C-T

Variant names:

• chr1-110917225-C-T
• rs1282023
• ENST00000802581.1:n.169+10329G>A

Variant summary

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

Score: -12 - Benign

-12

BP4_StrongBA1

The ENST00000802581.1(ENSG00000304336):​n.169+10329G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 151,964 control chromosomes in the GnomAD database, including 22,676 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 0.54 (22676 hom., cov: 31)
• Consequence: ENSG00000304336 ENST00000802581.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.659
• Publications: 1 publications found

Genes affected

ENSG00000304336 (HGNC:):

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]

LRIF1 Gene-Disease associations (from GenCC):

• facioscapulohumeral muscular dystrophy 3, digenic

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRIF1	XM_017001769.3	c.1869+32626G>A		intron_variant	Intron 3 of 3		XP_016857258.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304336	ENST00000802581.1	n.169+10329G>A		intron_variant	Intron 1 of 1
ENSG00000304336	ENST00000802582.1	n.169+10329G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81701 AN: 151846 Hom.: 22658 Cov.: 31

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.538 AC: 81770 AN: 151964 Hom.: 22676 Cov.: 31 AF XY: 0.538 AC XY: 39979 AN XY: 74278

African (AFR) AF: 0.665 AC: 27562 AN: 41426

American (AMR) AF: 0.523 AC: 7990 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1392 AN: 3472

East Asian (EAS) AF: 0.699 AC: 3613 AN: 5172

South Asian (SAS) AF: 0.467 AC: 2251 AN: 4818

European-Finnish (FIN) AF: 0.500 AC: 5273 AN: 10550

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32121 AN: 67948

Other (OTH) AF: 0.490 AC: 1034 AN: 2110

Alfa AF: 0.485 Hom.: 69722

Bravo AF: 0.547

Asia WGS AF: 0.509 AC: 1766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.3
DANN	Benign	0.38
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs1282023; hg19: chr1-111459847;