rs12567355

Variant names:

• chr1-110921002-G-A
• rs12567355
• ENST00000802581.1:n.169+6552C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-110921002-G-A
• chr1-110921002-G-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+6552C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0631 in 152,168 control chromosomes in the GnomAD database, including 332 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 0.063 (332 hom., cov: 32)
• Consequence: ENSG00000304336 ENST00000802581.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRIF1	XM_017001769.3	c.1869+28849C>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+6552C>T		intron_variant	Intron 1 of 1
ENSG00000304336	ENST00000802582.1	n.169+6552C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0630 AC: 9584 AN: 152050 Hom.: 331 Cov.: 32

Gnomad AFR AF: 0.0513

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0610

Gnomad ASJ AF: 0.0685

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0729

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.0604

Gnomad OTH AF: 0.0690

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

GnomAD4 genome AF: 0.0631 AC: 9602 AN: 152168 Hom.: 332 Cov.: 32 AF XY: 0.0646 AC XY: 4803 AN XY: 74380

African (AFR) AF: 0.0516 AC: 2143 AN: 41528

American (AMR) AF: 0.0609 AC: 931 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0685 AC: 238 AN: 3472

East Asian (EAS) AF: 0.143 AC: 741 AN: 5178

South Asian (SAS) AF: 0.0998 AC: 481 AN: 4818

European-Finnish (FIN) AF: 0.0729 AC: 771 AN: 10574

Middle Eastern (MID) AF: 0.0856 AC: 25 AN: 292

European-Non Finnish (NFE) AF: 0.0604 AC: 4107 AN: 68008

Other (OTH) AF: 0.0711 AC: 150 AN: 2110

Alfa AF: 0.0597 Hom.: 776

Bravo AF: 0.0616

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.45
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs12567355; hg19: chr1-111463624;