chr1-110914865-T-G

Variant names:

• chr1-110914865-T-G
• rs1282020
• XM_017001769.3:c.1869+34986A>C

Variant summary

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

The ENST00000802581.1(ENSG00000304336):​n.169+12689A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 152,052 control chromosomes in the GnomAD database, including 16,081 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 0.45 (16081 hom., cov: 32)
• Consequence: ENSG00000304336 ENST00000802581.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 5 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 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+12689A>C		intron	N/A
	ENSG00000304336	ENST00000802582.1		n.169+12689A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69098 AN: 151934 Hom.: 16077 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.455 AC: 69121 AN: 152052 Hom.: 16081 Cov.: 32 AF XY: 0.458 AC XY: 34054 AN XY: 74346

African (AFR) AF: 0.377 AC: 15639 AN: 41448

American (AMR) AF: 0.493 AC: 7540 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1388 AN: 3470

East Asian (EAS) AF: 0.688 AC: 3548 AN: 5160

South Asian (SAS) AF: 0.468 AC: 2261 AN: 4828

European-Finnish (FIN) AF: 0.500 AC: 5289 AN: 10574

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 32027 AN: 67966

Other (OTH) AF: 0.429 AC: 905 AN: 2110

Alfa AF: 0.464 Hom.: 9171

Bravo AF: 0.452

Asia WGS AF: 0.485 AC: 1684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	13
DANN	Benign	0.46
PhyloP100		0.15

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1282020;

hg19: chr1-111457487;