rs10520120

Variant summary

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

The ENST00000560484.1(ENSG00000259345):​n.68-76488G>A 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 0.0245 in 152,246 control chromosomes in the GnomAD database, including 102 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 0.025 ( 102 hom., cov: 32)

Consequence


ENST00000560484.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0110
Variant links:
Genes affected
LINC02694 (HGNC:33796): (long intergenic non-protein coding RNA 2694)

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=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105370777XR_007064588.1 linkuse as main transcriptn.518-76488G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000560484.1 linkuse as main transcriptn.68-76488G>A intron_variant, non_coding_transcript_variant 4
LINC02694ENST00000644461.1 linkuse as main transcriptn.159-24883C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0245
AC:
3729
AN:
152128
Hom.:
102
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0412
Gnomad AMI
AF:
0.00987
Gnomad AMR
AF:
0.0228
Gnomad ASJ
AF:
0.0127
Gnomad EAS
AF:
0.119
Gnomad SAS
AF:
0.105
Gnomad FIN
AF:
0.00207
Gnomad MID
AF:
0.0253
Gnomad NFE
AF:
0.00595
Gnomad OTH
AF:
0.0287
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0245
AC:
3735
AN:
152246
Hom.:
102
Cov.:
32
AF XY:
0.0259
AC XY:
1928
AN XY:
74426
show subpopulations
Gnomad4 AFR
AF:
0.0412
Gnomad4 AMR
AF:
0.0227
Gnomad4 ASJ
AF:
0.0127
Gnomad4 EAS
AF:
0.120
Gnomad4 SAS
AF:
0.106
Gnomad4 FIN
AF:
0.00207
Gnomad4 NFE
AF:
0.00594
Gnomad4 OTH
AF:
0.0293
Alfa
AF:
0.0140
Hom.:
2
Bravo
AF:
0.0254
Asia WGS
AF:
0.135
AC:
469
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
3.3
DANN
Benign
0.66

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: rs10520120; hg19: chr15-39440297; API