rs1548342

Variant names:

• chr1-110928432-G-A
• rs1548342
• XM_017001769.3:c.1869+21419C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-110928432-G-A
• chr1-110928432-G-C
• chr1-110928432-G-T

Variant summary

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

The XM_017001769.3(LRIF1):​c.1869+21419C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 151,962 control chromosomes in the GnomAD database, including 14,278 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 0.42 (14278 hom., cov: 31)
• Consequence: LRIF1 XM_017001769.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142
• Publications: 2 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)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63411 AN: 151842 Hom.: 14280 Cov.: 31

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.417 AC: 63421 AN: 151962 Hom.: 14278 Cov.: 31 AF XY: 0.421 AC XY: 31302 AN XY: 74266

African (AFR) AF: 0.250 AC: 10344 AN: 41444

American (AMR) AF: 0.479 AC: 7304 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1388 AN: 3464

East Asian (EAS) AF: 0.690 AC: 3569 AN: 5172

South Asian (SAS) AF: 0.465 AC: 2242 AN: 4822

European-Finnish (FIN) AF: 0.500 AC: 5271 AN: 10548

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.470 AC: 31946 AN: 67946

Other (OTH) AF: 0.401 AC: 845 AN: 2108

Alfa AF: 0.429 Hom.: 2465

Bravo AF: 0.410

Asia WGS AF: 0.475 AC: 1649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.43
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1548342; hg19: chr1-111471054;