rs1021055

Variant summary

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

The XR_007062357.1(LOC124902533):​n.562G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 152,010 control chromosomes in the GnomAD database, including 13,926 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 0.41 ( 13926 hom., cov: 32)

Consequence

LOC124902533
XR_007062357.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.372
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=-0.95).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124902533XR_007062357.1 linkuse as main transcriptn.562G>A non_coding_transcript_exon_variant 1/2

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.411
AC:
62439
AN:
151892
Hom.:
13910
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.233
Gnomad AMI
AF:
0.546
Gnomad AMR
AF:
0.489
Gnomad ASJ
AF:
0.391
Gnomad EAS
AF:
0.447
Gnomad SAS
AF:
0.510
Gnomad FIN
AF:
0.502
Gnomad MID
AF:
0.389
Gnomad NFE
AF:
0.477
Gnomad OTH
AF:
0.417
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.411
AC:
62495
AN:
152010
Hom.:
13926
Cov.:
32
AF XY:
0.415
AC XY:
30820
AN XY:
74276
show subpopulations
Gnomad4 AFR
AF:
0.233
Gnomad4 AMR
AF:
0.490
Gnomad4 ASJ
AF:
0.391
Gnomad4 EAS
AF:
0.447
Gnomad4 SAS
AF:
0.511
Gnomad4 FIN
AF:
0.502
Gnomad4 NFE
AF:
0.477
Gnomad4 OTH
AF:
0.422
Alfa
AF:
0.451
Hom.:
8449
Bravo
AF:
0.405
Asia WGS
AF:
0.493
AC:
1716
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.26
DANN
Benign
0.33

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: rs1021055; hg19: chr10-45073211; API