rs7902708

Variant summary

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

The ENST00000443523.3(LNCAROD):​n.123+75342C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 151,958 control chromosomes in the GnomAD database, including 3,103 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 0.17 ( 3103 hom., cov: 32)

Consequence

LNCAROD
ENST00000443523.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.686
Variant links:
Genes affected
LNCAROD (HGNC:50913): (lncRNA activating regulator of DKK1)

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=-0.56).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105378305NR_155748.1 linkn.95+75342C>G intron_variant Intron 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LNCARODENST00000443523.3 linkn.123+75342C>G intron_variant Intron 1 of 2 2
LNCARODENST00000448017.2 linkn.171+75338C>G intron_variant Intron 1 of 2 2
LNCARODENST00000647908.1 linkn.248+43902C>G intron_variant Intron 2 of 6

Frequencies

GnomAD3 genomes
AF:
0.174
AC:
26473
AN:
151838
Hom.:
3089
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.322
Gnomad AMI
AF:
0.0154
Gnomad AMR
AF:
0.122
Gnomad ASJ
AF:
0.0905
Gnomad EAS
AF:
0.196
Gnomad SAS
AF:
0.131
Gnomad FIN
AF:
0.155
Gnomad MID
AF:
0.0955
Gnomad NFE
AF:
0.108
Gnomad OTH
AF:
0.146
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.175
AC:
26538
AN:
151958
Hom.:
3103
Cov.:
32
AF XY:
0.175
AC XY:
13027
AN XY:
74282
show subpopulations
Gnomad4 AFR
AF:
0.323
Gnomad4 AMR
AF:
0.122
Gnomad4 ASJ
AF:
0.0905
Gnomad4 EAS
AF:
0.197
Gnomad4 SAS
AF:
0.131
Gnomad4 FIN
AF:
0.155
Gnomad4 NFE
AF:
0.108
Gnomad4 OTH
AF:
0.150
Alfa
AF:
0.145
Hom.:
272
Bravo
AF:
0.177
Asia WGS
AF:
0.192
AC:
667
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.56
CADD
Benign
14
DANN
Benign
0.59

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: rs7902708; hg19: chr10-54439728; API