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GeneBe

22-46143831-C-T

Variant summary

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

The XR_007068140.1(LOC124905138):n.398G>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 0.996 in 152,372 control chromosomes in the GnomAD database, including 75,508 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 1.0 ( 75508 hom., cov: 35)

Consequence

LOC124905138
XR_007068140.1 non_coding_transcript_exon

Scores

1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.233
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=-0.8).
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 = 0.991 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124905138XR_007068140.1 linkuse as main transcriptn.398G>A 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:
0.996
AC:
151573
AN:
152254
Hom.:
75449
Cov.:
35
show subpopulations
Gnomad AFR
AF:
0.999
Gnomad AMI
AF:
0.980
Gnomad AMR
AF:
0.996
Gnomad ASJ
AF:
0.999
Gnomad EAS
AF:
1.00
Gnomad SAS
AF:
1.00
Gnomad FIN
AF:
0.974
Gnomad MID
AF:
1.00
Gnomad NFE
AF:
0.996
Gnomad OTH
AF:
0.997
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:
0.996
AC:
151691
AN:
152372
Hom.:
75508
Cov.:
35
AF XY:
0.995
AC XY:
74103
AN XY:
74504
show subpopulations
Gnomad4 AFR
AF:
0.999
Gnomad4 AMR
AF:
0.996
Gnomad4 ASJ
AF:
0.999
Gnomad4 EAS
AF:
1.00
Gnomad4 SAS
AF:
1.00
Gnomad4 FIN
AF:
0.974
Gnomad4 NFE
AF:
0.996
Gnomad4 OTH
AF:
0.997
Alfa
AF:
0.996
Hom.:
8925
Bravo
AF:
0.997

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
Cadd
Benign
2.5

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: rs135559; hg19: chr22-46539706; API