rs1936942

Variant names:

• chr1-110907786-G-A
• rs1936942
• ENST00000802581.1:n.169+19768C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-110907786-G-A
• chr1-110907786-G-C
• chr1-110907786-G-T

Variant summary

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

The ENST00000802581.1(ENSG00000304336):​n.169+19768C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,880 control chromosomes in the GnomAD database, including 20,370 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 0.51 (20370 hom., cov: 31)
• Consequence: ENSG00000304336 ENST00000802581.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 7 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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRIF1	XM_017001769.3	c.1870-30101C>T		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+19768C>T		intron_variant	Intron 1 of 1
ENSG00000304336	ENST00000802582.1	n.170-16942C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77882 AN: 151760 Hom.: 20338 Cov.: 31

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.513 AC: 77962 AN: 151880 Hom.: 20370 Cov.: 31 AF XY: 0.511 AC XY: 37951 AN XY: 74232

African (AFR) AF: 0.432 AC: 17891 AN: 41408

American (AMR) AF: 0.517 AC: 7889 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2223 AN: 3466

East Asian (EAS) AF: 0.312 AC: 1610 AN: 5164

South Asian (SAS) AF: 0.565 AC: 2716 AN: 4810

European-Finnish (FIN) AF: 0.520 AC: 5474 AN: 10524

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.563 AC: 38259 AN: 67932

Other (OTH) AF: 0.564 AC: 1187 AN: 2104

Alfa AF: 0.557 Hom.: 37193

Bravo AF: 0.508

Asia WGS AF: 0.512 AC: 1781 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.28
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs1936942; hg19: chr1-111450408;