XR_001739475.2:n.207C>G

Variant summary

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

The XR_001739475.2(LOC102724072):​n.207C>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 0.666 in 152,102 control chromosomes in the GnomAD database, including 34,137 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 0.67 ( 34137 hom., cov: 32)

Consequence

LOC102724072
XR_001739475.2 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.379
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=-0.82).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC102724072XR_001739475.2 linkn.207C>G non_coding_transcript_exon_variant Exon 1 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.666
AC:
101184
AN:
151984
Hom.:
34109
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.685
Gnomad AMI
AF:
0.691
Gnomad AMR
AF:
0.725
Gnomad ASJ
AF:
0.573
Gnomad EAS
AF:
0.965
Gnomad SAS
AF:
0.705
Gnomad FIN
AF:
0.724
Gnomad MID
AF:
0.630
Gnomad NFE
AF:
0.611
Gnomad OTH
AF:
0.637
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.666
AC:
101259
AN:
152102
Hom.:
34137
Cov.:
32
AF XY:
0.675
AC XY:
50180
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.685
Gnomad4 AMR
AF:
0.726
Gnomad4 ASJ
AF:
0.573
Gnomad4 EAS
AF:
0.965
Gnomad4 SAS
AF:
0.706
Gnomad4 FIN
AF:
0.724
Gnomad4 NFE
AF:
0.611
Gnomad4 OTH
AF:
0.632
Alfa
AF:
0.609
Hom.:
14161
Bravo
AF:
0.667
Asia WGS
AF:
0.812
AC:
2818
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
7.4
DANN
Benign
0.67

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: rs4233949; hg19: chr2-54659707; API