rs12567355

chr1-110921002-G-Achr1-110921002-G-C

Variant summary

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

The XM_017001769.3(LRIF1):c.1869+28849C>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: LRIF1 XM_017001769.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

Genes affected

LRIF1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LRIF1	XM_017001769.3	c.1869+28849C>T		intron_variant

Ensembl

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

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

Gnomad4 AFR AF: 0.0516

Gnomad4 AMR AF: 0.0609

Gnomad4 ASJ AF: 0.0685

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.0998

Gnomad4 FIN AF: 0.0729

Gnomad4 NFE AF: 0.0604

Gnomad4 OTH AF: 0.0711

Alfa AF: 0.0583 Hom.: 281

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12567355; hg19: chr1-111463624;