rs1539635

Positions:

Variant summary

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

The XR_007065350.1(LOC124903820):​n.2220G>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 0.548 in 151,898 control chromosomes in the GnomAD database, including 24,036 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 0.55 ( 24036 hom., cov: 32)

Consequence

LOC124903820
XR_007065350.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.252
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=-0.89).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC124903820XR_007065350.1 linkuse as main transcriptn.2220G>A non_coding_transcript_exon_variant 2/2
LOC124903820XR_007065351.1 linkuse as main transcriptn.1502G>A non_coding_transcript_exon_variant 3/3
use as main transcriptn.1161712G>A intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.548
AC:
83163
AN:
151780
Hom.:
24015
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.372
Gnomad AMI
AF:
0.723
Gnomad AMR
AF:
0.703
Gnomad ASJ
AF:
0.684
Gnomad EAS
AF:
0.537
Gnomad SAS
AF:
0.588
Gnomad FIN
AF:
0.513
Gnomad MID
AF:
0.604
Gnomad NFE
AF:
0.613
Gnomad OTH
AF:
0.588
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.548
AC:
83213
AN:
151898
Hom.:
24036
Cov.:
32
AF XY:
0.547
AC XY:
40588
AN XY:
74262
show subpopulations
Gnomad4 AFR
AF:
0.372
Gnomad4 AMR
AF:
0.704
Gnomad4 ASJ
AF:
0.684
Gnomad4 EAS
AF:
0.538
Gnomad4 SAS
AF:
0.587
Gnomad4 FIN
AF:
0.513
Gnomad4 NFE
AF:
0.613
Gnomad4 OTH
AF:
0.592
Alfa
AF:
0.562
Hom.:
3072
Bravo
AF:
0.555
Asia WGS
AF:
0.585
AC:
2034
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.90
DANN
Benign
0.76

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: rs1539635; hg19: chr1-1097092; API