1-110917225-C-T

Position:

• chr1-110917225-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_017001769.3(LRIF1):​c.1869+32626G>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: LRIF1 XM_017001769.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.659

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 Benign. Variant got -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/exons	MANE	Protein	UniProt
LRIF1	XM_017001769.3	c.1869+32626G>A		intron_variant			XP_016857258.1
		n.110917225C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.665

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.490

Alfa AF: 0.472 Hom.: 31305

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1282023; hg19: chr1-111459847;