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GeneBe

rs585017

Positions:

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000702995.1(ENSG00000290108):​n.23C>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 0.764 in 151,996 control chromosomes in the GnomAD database, including 44,520 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.76 ( 44520 hom., cov: 33)

Consequence


ENST00000702995.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.202
Variant links:
Genes affected

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 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=-0.54).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 2-20446871-G-A is Benign according to our data. Variant chr2-20446871-G-A is described in ClinVar as [Benign]. Clinvar id is 1271789.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 (EAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000702995.1 linkuse as main transcriptn.23C>T non_coding_transcript_exon_variant 1/1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.764
AC:
116005
AN:
151878
Hom.:
44463
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.797
Gnomad AMI
AF:
0.616
Gnomad AMR
AF:
0.809
Gnomad ASJ
AF:
0.694
Gnomad EAS
AF:
0.920
Gnomad SAS
AF:
0.811
Gnomad FIN
AF:
0.751
Gnomad MID
AF:
0.782
Gnomad NFE
AF:
0.726
Gnomad OTH
AF:
0.764
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:
0.764
AC:
116123
AN:
151996
Hom.:
44520
Cov.:
33
AF XY:
0.769
AC XY:
57126
AN XY:
74288
show subpopulations
Gnomad4 AFR
AF:
0.797
Gnomad4 AMR
AF:
0.809
Gnomad4 ASJ
AF:
0.694
Gnomad4 EAS
AF:
0.920
Gnomad4 SAS
AF:
0.812
Gnomad4 FIN
AF:
0.751
Gnomad4 NFE
AF:
0.726
Gnomad4 OTH
AF:
0.766
Alfa
AF:
0.651
Hom.:
1809
Bravo
AF:
0.770
Asia WGS
AF:
0.860
AC:
2988
AN:
3476

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 testingGeneDxMay 14, 2021This variant is associated with the following publications: (PMID: 16642435) -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.54
CADD
Benign
9.2
DANN
Benign
0.95

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: rs585017; hg19: chr2-20646632; API