1-110917225-C-T

Variant names:

• chr1-110917225-C-T
• rs1282023
• XM_017001769.3:c.1869+32626G>A

Variant summary

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

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

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)

ENSG00000304336 (HGNC:):

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000802581.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304336	ENST00000802581.1		n.169+10329G>A		intron	N/A
	ENSG00000304336	ENST00000802582.1		n.169+10329G>A		intron	N/A

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 v4.9

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;