Menu
GeneBe

rs135561

chr22-46143764-G-Achr22-46143764-G-Cchr22-46143764-G-T

Variant summary

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

The XR_007068140.1(LOC124905138):n.465C>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 0.366 in 152,114 control chromosomes in the GnomAD database, including 12,300 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 0.37 ( 12300 hom., cov: 33)

Consequence

LOC124905138
XR_007068140.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.44
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 (Cadd=14.19).
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 = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124905138XR_007068140.1 linkuse as main transcriptn.465C>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:
0.366
AC:
55578
AN:
151996
Hom.:
12272
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.617
Gnomad AMI
AF:
0.421
Gnomad AMR
AF:
0.237
Gnomad ASJ
AF:
0.225
Gnomad EAS
AF:
0.0810
Gnomad SAS
AF:
0.207
Gnomad FIN
AF:
0.256
Gnomad MID
AF:
0.234
Gnomad NFE
AF:
0.299
Gnomad OTH
AF:
0.343
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:
0.366
AC:
55657
AN:
152114
Hom.:
12300
Cov.:
33
AF XY:
0.356
AC XY:
26483
AN XY:
74380
show subpopulations
Gnomad4 AFR
AF:
0.617
Gnomad4 AMR
AF:
0.236
Gnomad4 ASJ
AF:
0.225
Gnomad4 EAS
AF:
0.0810
Gnomad4 SAS
AF:
0.207
Gnomad4 FIN
AF:
0.256
Gnomad4 NFE
AF:
0.299
Gnomad4 OTH
AF:
0.339
Alfa
AF:
0.329
Hom.:
1502
Bravo
AF:
0.377

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
Cadd
Benign
14

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: rs135561; hg19: -; API