rs2196586

Variant summary

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

The XR_928910.2(LOC105375849):​n.54+262A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 151,880 control chromosomes in the GnomAD database, including 45,395 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 0.77 ( 45395 hom., cov: 29)

Consequence

LOC105375849
XR_928910.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.567
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=-1.02).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105375849XR_928910.2 linkuse as main transcriptn.54+262A>G intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.772
AC:
117185
AN:
151762
Hom.:
45366
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.739
Gnomad AMI
AF:
0.810
Gnomad AMR
AF:
0.798
Gnomad ASJ
AF:
0.801
Gnomad EAS
AF:
0.869
Gnomad SAS
AF:
0.867
Gnomad FIN
AF:
0.804
Gnomad MID
AF:
0.823
Gnomad NFE
AF:
0.765
Gnomad OTH
AF:
0.774
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.772
AC:
117268
AN:
151880
Hom.:
45395
Cov.:
29
AF XY:
0.775
AC XY:
57476
AN XY:
74206
show subpopulations
Gnomad4 AFR
AF:
0.739
Gnomad4 AMR
AF:
0.798
Gnomad4 ASJ
AF:
0.801
Gnomad4 EAS
AF:
0.869
Gnomad4 SAS
AF:
0.868
Gnomad4 FIN
AF:
0.804
Gnomad4 NFE
AF:
0.765
Gnomad4 OTH
AF:
0.777
Alfa
AF:
0.770
Hom.:
8416
Bravo
AF:
0.769
Asia WGS
AF:
0.873
AC:
3036
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
0.97
DANN
Benign
0.51

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: rs2196586; hg19: chr8-57347126; API