GeneBe

7-142307367-AGTGTGTGTGTGTGTGTGT-AGT

Position:

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.020 ( 54 hom., cov: 0)

Consequence


intergenic_region

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.60
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0196 (2873/146322) while in subpopulation NFE AF= 0.031 (2055/66374). AF 95% confidence interval is 0.0298. There are 54 homozygotes in gnomad4. There are 1397 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 54 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.142307368_142307383delGTGTGTGTGTGTGTGT intergenic_region
TRB use as main transcriptn.142307385_142307400delTGTGTGTGTGTGTGTG intragenic_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.0196
AC:
2873
AN:
146216
Hom.:
54
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00553
Gnomad AMI
AF:
0.00111
Gnomad AMR
AF:
0.0129
Gnomad ASJ
AF:
0.0152
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00601
Gnomad FIN
AF:
0.0310
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0310
Gnomad OTH
AF:
0.0171
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0196
AC:
2873
AN:
146322
Hom.:
54
Cov.:
0
AF XY:
0.0197
AC XY:
1397
AN XY:
71052
show subpopulations
Gnomad4 AFR
AF:
0.00552
Gnomad4 AMR
AF:
0.0129
Gnomad4 ASJ
AF:
0.0152
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00602
Gnomad4 FIN
AF:
0.0310
Gnomad4 NFE
AF:
0.0310
Gnomad4 OTH
AF:
0.0169

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs3222967; hg19: chr7-142007188; API