1-7867921-C-T

Variant summary

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

The XM_011540537.3(UTS2):​c.-74-14416G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.894 in 152,212 control chromosomes in the GnomAD database, including 60,982 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 0.89 ( 60982 hom., cov: 32)

Consequence

UTS2
XM_011540537.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.372
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
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
UTS2XM_011540537.3 linkuse as main transcriptc.-74-14416G>A intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.894
AC:
135945
AN:
152094
Hom.:
60928
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.849
Gnomad AMI
AF:
0.818
Gnomad AMR
AF:
0.898
Gnomad ASJ
AF:
0.944
Gnomad EAS
AF:
0.962
Gnomad SAS
AF:
0.921
Gnomad FIN
AF:
0.961
Gnomad MID
AF:
0.851
Gnomad NFE
AF:
0.901
Gnomad OTH
AF:
0.896
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.894
AC:
136056
AN:
152212
Hom.:
60982
Cov.:
32
AF XY:
0.898
AC XY:
66793
AN XY:
74414
show subpopulations
Gnomad4 AFR
AF:
0.849
Gnomad4 AMR
AF:
0.899
Gnomad4 ASJ
AF:
0.944
Gnomad4 EAS
AF:
0.961
Gnomad4 SAS
AF:
0.920
Gnomad4 FIN
AF:
0.961
Gnomad4 NFE
AF:
0.901
Gnomad4 OTH
AF:
0.897
Alfa
AF:
0.905
Hom.:
82777
Bravo
AF:
0.888
Asia WGS
AF:
0.933
AC:
3245
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.31
DANN
Benign
0.31

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: rs579992; hg19: chr1-7927981; API