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GeneBe

rs1936942

chr1-110907786-G-Achr1-110907786-G-Cchr1-110907786-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XM_017001769.3(LRIF1):c.1870-30101C>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

LRIF1
XM_017001769.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.928
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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/exons MANE UniProt
LRIF1XM_017001769.3 linkuse as main transcriptc.1870-30101C>T intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.513
AC:
77882
AN:
151760
Hom.:
20338
Cov.:
31
show subpopulations
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.513
AC:
77962
AN:
151880
Hom.:
20370
Cov.:
31
AF XY:
0.511
AC XY:
37951
AN XY:
74232
show subpopulations
Gnomad4 AFR
AF:
0.432
Gnomad4 AMR
AF:
0.517
Gnomad4 ASJ
AF:
0.641
Gnomad4 EAS
AF:
0.312
Gnomad4 SAS
AF:
0.565
Gnomad4 FIN
AF:
0.520
Gnomad4 NFE
AF:
0.563
Gnomad4 OTH
AF:
0.564
Alfa
AF:
0.558
Hom.:
31467
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

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1936942; hg19: chr1-111450408; API