3-117508453-T-G

Variant summary

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

The XR_924361.3(LOC105374056):​n.25133T>G 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 0.13 in 152,098 control chromosomes in the GnomAD database, including 1,627 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 0.13 ( 1627 hom., cov: 32)

Consequence

LOC105374056
XR_924361.3 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.302
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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC105374056XR_007096021.1 linkn.25133T>G non_coding_transcript_exon_variant 1/3
LOC105374056XR_924361.3 linkn.25133T>G non_coding_transcript_exon_variant 1/4

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.130
AC:
19810
AN:
151980
Hom.:
1627
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0467
Gnomad AMI
AF:
0.342
Gnomad AMR
AF:
0.104
Gnomad ASJ
AF:
0.200
Gnomad EAS
AF:
0.000579
Gnomad SAS
AF:
0.0522
Gnomad FIN
AF:
0.175
Gnomad MID
AF:
0.130
Gnomad NFE
AF:
0.189
Gnomad OTH
AF:
0.126
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.130
AC:
19807
AN:
152098
Hom.:
1627
Cov.:
32
AF XY:
0.127
AC XY:
9455
AN XY:
74322
show subpopulations
Gnomad4 AFR
AF:
0.0466
Gnomad4 AMR
AF:
0.104
Gnomad4 ASJ
AF:
0.200
Gnomad4 EAS
AF:
0.000580
Gnomad4 SAS
AF:
0.0522
Gnomad4 FIN
AF:
0.175
Gnomad4 NFE
AF:
0.189
Gnomad4 OTH
AF:
0.124
Alfa
AF:
0.0894
Hom.:
131
Bravo
AF:
0.123
Asia WGS
AF:
0.0310
AC:
109
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
3.8
DANN
Benign
0.60

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: rs45530132; hg19: chr3-117227300; API