rs35749

Variant summary

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

The XR_007063427.1(LINC02456):​n.34902+62517T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,160 control chromosomes in the GnomAD database, including 53,303 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 0.84 ( 53303 hom., cov: 31)

Consequence

LINC02456
XR_007063427.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.45
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=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LINC02456XR_007063427.1 linkuse as main transcriptn.34902+62517T>C intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.836
AC:
127037
AN:
152042
Hom.:
53268
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.763
Gnomad AMI
AF:
0.829
Gnomad AMR
AF:
0.898
Gnomad ASJ
AF:
0.845
Gnomad EAS
AF:
0.945
Gnomad SAS
AF:
0.877
Gnomad FIN
AF:
0.820
Gnomad MID
AF:
0.845
Gnomad NFE
AF:
0.855
Gnomad OTH
AF:
0.866
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.835
AC:
127126
AN:
152160
Hom.:
53303
Cov.:
31
AF XY:
0.837
AC XY:
62282
AN XY:
74372
show subpopulations
Gnomad4 AFR
AF:
0.763
Gnomad4 AMR
AF:
0.899
Gnomad4 ASJ
AF:
0.845
Gnomad4 EAS
AF:
0.944
Gnomad4 SAS
AF:
0.876
Gnomad4 FIN
AF:
0.820
Gnomad4 NFE
AF:
0.855
Gnomad4 OTH
AF:
0.868
Alfa
AF:
0.844
Hom.:
10335
Bravo
AF:
0.841
Asia WGS
AF:
0.932
AC:
3240
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.46
DANN
Benign
0.35

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: rs35749; hg19: chr12-102940183; API