rs6092179

Variant summary

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

The XR_936887.2(LOC105372677):​n.78C>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 0.212 in 151,738 control chromosomes in the GnomAD database, including 3,713 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 0.21 ( 3713 hom., cov: 32)

Consequence

LOC105372677
XR_936887.2 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.514
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=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105372677XR_936887.2 linkuse as main transcriptn.78C>A non_coding_transcript_exon_variant 1/3

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.212
AC:
32199
AN:
151620
Hom.:
3703
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.298
Gnomad AMI
AF:
0.181
Gnomad AMR
AF:
0.157
Gnomad ASJ
AF:
0.287
Gnomad EAS
AF:
0.135
Gnomad SAS
AF:
0.216
Gnomad FIN
AF:
0.173
Gnomad MID
AF:
0.301
Gnomad NFE
AF:
0.181
Gnomad OTH
AF:
0.220
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.212
AC:
32231
AN:
151738
Hom.:
3713
Cov.:
32
AF XY:
0.212
AC XY:
15722
AN XY:
74122
show subpopulations
Gnomad4 AFR
AF:
0.298
Gnomad4 AMR
AF:
0.156
Gnomad4 ASJ
AF:
0.287
Gnomad4 EAS
AF:
0.136
Gnomad4 SAS
AF:
0.215
Gnomad4 FIN
AF:
0.173
Gnomad4 NFE
AF:
0.181
Gnomad4 OTH
AF:
0.218
Alfa
AF:
0.190
Hom.:
5388
Bravo
AF:
0.213
Asia WGS
AF:
0.177
AC:
613
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.53
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: rs6092179; hg19: chr20-54379033; API