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GeneBe

rs282071

Positions:

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4BP6_ModerateBA1

The XR_007059680.1(LOC124901363):​n.568C>T 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 0.631 in 151,974 control chromosomes in the GnomAD database, including 30,564 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.63 ( 30564 hom., cov: 32)

Consequence

LOC124901363
XR_007059680.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.38
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.18).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 6-90587361-C-T is Benign according to our data. Variant chr6-90587361-C-T is described in ClinVar as [Benign]. Clinvar id is 1228113.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124901363XR_007059680.1 linkuse as main transcriptn.568C>T non_coding_transcript_exon_variant 1/2
LOC124901363XR_007059679.1 linkuse as main transcriptn.149C>T non_coding_transcript_exon_variant 1/3
LOC124901363XR_007059681.1 linkuse as main transcriptn.171C>T non_coding_transcript_exon_variant 1/2

Ensembl

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

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.631
AC:
95788
AN:
151856
Hom.:
30550
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.579
Gnomad AMI
AF:
0.584
Gnomad AMR
AF:
0.587
Gnomad ASJ
AF:
0.783
Gnomad EAS
AF:
0.433
Gnomad SAS
AF:
0.648
Gnomad FIN
AF:
0.631
Gnomad MID
AF:
0.742
Gnomad NFE
AF:
0.677
Gnomad OTH
AF:
0.669
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.631
AC:
95835
AN:
151974
Hom.:
30564
Cov.:
32
AF XY:
0.626
AC XY:
46489
AN XY:
74270
show subpopulations
Gnomad4 AFR
AF:
0.578
Gnomad4 AMR
AF:
0.587
Gnomad4 ASJ
AF:
0.783
Gnomad4 EAS
AF:
0.433
Gnomad4 SAS
AF:
0.648
Gnomad4 FIN
AF:
0.631
Gnomad4 NFE
AF:
0.677
Gnomad4 OTH
AF:
0.674
Alfa
AF:
0.654
Hom.:
7897
Bravo
AF:
0.621
Asia WGS
AF:
0.570
AC:
1984
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxNov 12, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.18
CADD
Benign
7.5
DANN
Benign
0.94

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: rs282071; hg19: chr6-91297080; COSMIC: COSV65235343; API