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GeneBe

rs1282020

chr1-110914865-T-G

Variant summary

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

The XM_017001769.3(LRIF1):c.1869+34986A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 152,052 control chromosomes in the GnomAD database, including 16,081 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 0.45 ( 16081 hom., cov: 32)

Consequence

LRIF1
XM_017001769.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.147
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=-0.82).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LRIF1XM_017001769.3 linkuse as main transcriptc.1869+34986A>C 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:
0.455
AC:
69098
AN:
151934
Hom.:
16077
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.378
Gnomad AMI
AF:
0.462
Gnomad AMR
AF:
0.493
Gnomad ASJ
AF:
0.400
Gnomad EAS
AF:
0.688
Gnomad SAS
AF:
0.468
Gnomad FIN
AF:
0.500
Gnomad MID
AF:
0.370
Gnomad NFE
AF:
0.471
Gnomad OTH
AF:
0.435
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:
0.455
AC:
69121
AN:
152052
Hom.:
16081
Cov.:
32
AF XY:
0.458
AC XY:
34054
AN XY:
74346
show subpopulations
Gnomad4 AFR
AF:
0.377
Gnomad4 AMR
AF:
0.493
Gnomad4 ASJ
AF:
0.400
Gnomad4 EAS
AF:
0.688
Gnomad4 SAS
AF:
0.468
Gnomad4 FIN
AF:
0.500
Gnomad4 NFE
AF:
0.471
Gnomad4 OTH
AF:
0.429
Alfa
AF:
0.464
Hom.:
8261
Bravo
AF:
0.452
Asia WGS
AF:
0.485
AC:
1684
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
Cadd
Benign
13
Dann
Benign
0.46

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: rs1282020; hg19: chr1-111457487; API