12-126960604-G-A

Variant summary

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

The ENST00000512624.6(LINC02405):​n.685+15235C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0669 in 152,190 control chromosomes in the GnomAD database, including 892 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 0.067 ( 892 hom., cov: 33)

Consequence

LINC02405
ENST00000512624.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.607
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
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LINC02405NR_104646.1 linkuse as main transcriptn.685+15235C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC02405ENST00000512624.6 linkuse as main transcriptn.685+15235C>T intron_variant 1
LINC02405ENST00000651439.2 linkuse as main transcriptn.731+15235C>T intron_variant
LINC02405ENST00000656033.1 linkuse as main transcriptn.699+15235C>T intron_variant

Frequencies

GnomAD3 genomes
AF:
0.0667
AC:
10146
AN:
152072
Hom.:
885
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.200
Gnomad AMI
AF:
0.00987
Gnomad AMR
AF:
0.0291
Gnomad ASJ
AF:
0.0372
Gnomad EAS
AF:
0.111
Gnomad SAS
AF:
0.0367
Gnomad FIN
AF:
0.00236
Gnomad MID
AF:
0.0506
Gnomad NFE
AF:
0.00571
Gnomad OTH
AF:
0.0512
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0669
AC:
10189
AN:
152190
Hom.:
892
Cov.:
33
AF XY:
0.0668
AC XY:
4968
AN XY:
74422
show subpopulations
Gnomad4 AFR
AF:
0.200
Gnomad4 AMR
AF:
0.0291
Gnomad4 ASJ
AF:
0.0372
Gnomad4 EAS
AF:
0.111
Gnomad4 SAS
AF:
0.0365
Gnomad4 FIN
AF:
0.00236
Gnomad4 NFE
AF:
0.00571
Gnomad4 OTH
AF:
0.0578
Alfa
AF:
0.0409
Hom.:
60
Bravo
AF:
0.0761
Asia WGS
AF:
0.100
AC:
349
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
7.6
DANN
Benign
0.77

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: rs1456160; hg19: chr12-127445150; API