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GeneBe

rs2732549

chr11-35066852-G-Achr11-35066852-G-C

Variant summary

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

The ENST00000702237.1(ENSG00000289526):n.52C>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 0.681 in 151,830 control chromosomes in the GnomAD database, including 37,021 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 0.68 ( 37021 hom., cov: 30)

Consequence


ENST00000702237.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.791
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
?
    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=-0.94).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105376626XR_001748180.2 linkuse as main transcriptn.340C>T non_coding_transcript_exon_variant 1/4
LOC105376626XR_007062653.1 linkuse as main transcriptn.340C>T non_coding_transcript_exon_variant 1/5
LOC105376626XR_007062654.1 linkuse as main transcriptn.340C>T non_coding_transcript_exon_variant 1/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000702237.1 linkuse as main transcriptn.52C>T non_coding_transcript_exon_variant 1/3
ENST00000685560.1 linkuse as main transcriptn.72C>T non_coding_transcript_exon_variant 1/3
ENST00000687081.1 linkuse as main transcriptn.341C>T non_coding_transcript_exon_variant 1/2
ENST00000701115.1 linkuse as main transcriptn.52C>T non_coding_transcript_exon_variant 1/3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.681
AC:
103343
AN:
151712
Hom.:
36964
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.905
Gnomad AMI
AF:
0.569
Gnomad AMR
AF:
0.668
Gnomad ASJ
AF:
0.636
Gnomad EAS
AF:
0.791
Gnomad SAS
AF:
0.780
Gnomad FIN
AF:
0.538
Gnomad MID
AF:
0.722
Gnomad NFE
AF:
0.558
Gnomad OTH
AF:
0.679
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:
0.681
AC:
103453
AN:
151830
Hom.:
37021
Cov.:
30
AF XY:
0.684
AC XY:
50716
AN XY:
74166
show subpopulations
Gnomad4 AFR
AF:
0.906
Gnomad4 AMR
AF:
0.669
Gnomad4 ASJ
AF:
0.636
Gnomad4 EAS
AF:
0.791
Gnomad4 SAS
AF:
0.779
Gnomad4 FIN
AF:
0.538
Gnomad4 NFE
AF:
0.558
Gnomad4 OTH
AF:
0.682
Alfa
AF:
0.579
Hom.:
23171
Bravo
AF:
0.697
Asia WGS
AF:
0.777
AC:
2704
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
Cadd
Benign
7.6
Dann
Benign
0.53

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: rs2732549; hg19: chr11-35088399; API