13-89206246-A-G

Variant summary

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

The ENST00000653072.1(LINC00440):​n.28+24895A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 152,030 control chromosomes in the GnomAD database, including 44,012 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 0.76 ( 44012 hom., cov: 32)

Consequence

LINC00440
ENST00000653072.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.615
Variant links:
Genes affected
LINC00440 (HGNC:42777): (long intergenic non-protein coding RNA 440)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC00440ENST00000653072.1 linkn.28+24895A>G intron_variant Intron 1 of 3

Frequencies

GnomAD3 genomes
AF:
0.758
AC:
115134
AN:
151912
Hom.:
43988
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.710
Gnomad AMI
AF:
0.837
Gnomad AMR
AF:
0.811
Gnomad ASJ
AF:
0.796
Gnomad EAS
AF:
0.623
Gnomad SAS
AF:
0.792
Gnomad FIN
AF:
0.642
Gnomad MID
AF:
0.864
Gnomad NFE
AF:
0.797
Gnomad OTH
AF:
0.784
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.758
AC:
115208
AN:
152030
Hom.:
44012
Cov.:
32
AF XY:
0.752
AC XY:
55844
AN XY:
74298
show subpopulations
Gnomad4 AFR
AF:
0.710
Gnomad4 AMR
AF:
0.811
Gnomad4 ASJ
AF:
0.796
Gnomad4 EAS
AF:
0.623
Gnomad4 SAS
AF:
0.791
Gnomad4 FIN
AF:
0.642
Gnomad4 NFE
AF:
0.797
Gnomad4 OTH
AF:
0.783
Alfa
AF:
0.794
Hom.:
59925
Bravo
AF:
0.767
Asia WGS
AF:
0.716
AC:
2492
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
4.0
DANN
Benign
0.80

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: rs2120871; hg19: chr13-89858500; API