Menu
GeneBe

rs1317423

Positions:

Variant summary

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

The XR_007058516.1(LOC124900882):​n.2109G>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 0.489 in 151,980 control chromosomes in the GnomAD database, including 18,970 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 0.49 ( 18970 hom., cov: 32)

Consequence

LOC124900882
XR_007058516.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.811
Variant links:
Genes affected
FRG1-DT (HGNC:51590): (FRG1 divergent transcript)

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=-0.89).
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 = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124900882XR_007058516.1 linkuse as main transcriptn.2109G>A non_coding_transcript_exon_variant 2/2
FRG1-DTNR_149039.1 linkuse as main transcriptn.1407-19231G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FRG1-DTENST00000660244.1 linkuse as main transcriptn.1407-19231G>A intron_variant, non_coding_transcript_variant
FRG1-DTENST00000506276.5 linkuse as main transcriptn.240-4179G>A intron_variant, non_coding_transcript_variant 3
FRG1-DTENST00000656003.1 linkuse as main transcriptn.668-19231G>A intron_variant, non_coding_transcript_variant
FRG1-DTENST00000657714.1 linkuse as main transcriptn.757-19231G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.489
AC:
74249
AN:
151860
Hom.:
18964
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.354
Gnomad AMI
AF:
0.395
Gnomad AMR
AF:
0.611
Gnomad ASJ
AF:
0.432
Gnomad EAS
AF:
0.816
Gnomad SAS
AF:
0.550
Gnomad FIN
AF:
0.489
Gnomad MID
AF:
0.513
Gnomad NFE
AF:
0.517
Gnomad OTH
AF:
0.519
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:
0.489
AC:
74296
AN:
151980
Hom.:
18970
Cov.:
32
AF XY:
0.490
AC XY:
36384
AN XY:
74290
show subpopulations
Gnomad4 AFR
AF:
0.354
Gnomad4 AMR
AF:
0.611
Gnomad4 ASJ
AF:
0.432
Gnomad4 EAS
AF:
0.816
Gnomad4 SAS
AF:
0.548
Gnomad4 FIN
AF:
0.489
Gnomad4 NFE
AF:
0.517
Gnomad4 OTH
AF:
0.522
Alfa
AF:
0.515
Hom.:
15871
Bravo
AF:
0.492
Asia WGS
AF:
0.648
AC:
2251
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.83
DANN
Benign
0.53

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: rs1317423; hg19: chr4-190706132; API