rs1360286

Variant summary

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

The XR_001746634.2(LOC107987053):​n.471+24676C>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 0.248 in 151,692 control chromosomes in the GnomAD database, including 4,933 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 0.25 ( 4933 hom., cov: 30)

Consequence

LOC107987053
XR_001746634.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.41
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=-1.03).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC107987053XR_001746634.2 linkuse as main transcriptn.471+24676C>A intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.248
AC:
37620
AN:
151572
Hom.:
4925
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.284
Gnomad AMI
AF:
0.166
Gnomad AMR
AF:
0.298
Gnomad ASJ
AF:
0.239
Gnomad EAS
AF:
0.471
Gnomad SAS
AF:
0.157
Gnomad FIN
AF:
0.211
Gnomad MID
AF:
0.225
Gnomad NFE
AF:
0.213
Gnomad OTH
AF:
0.246
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.248
AC:
37675
AN:
151692
Hom.:
4933
Cov.:
30
AF XY:
0.248
AC XY:
18408
AN XY:
74104
show subpopulations
Gnomad4 AFR
AF:
0.284
Gnomad4 AMR
AF:
0.298
Gnomad4 ASJ
AF:
0.239
Gnomad4 EAS
AF:
0.471
Gnomad4 SAS
AF:
0.159
Gnomad4 FIN
AF:
0.211
Gnomad4 NFE
AF:
0.213
Gnomad4 OTH
AF:
0.245
Alfa
AF:
0.223
Hom.:
2897
Bravo
AF:
0.260
Asia WGS
AF:
0.307
AC:
1067
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
2.3
DANN
Benign
0.32

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: rs1360286; hg19: chr9-21293631; API