rs10805650

Variant summary

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

The XR_001742615.2(LOC105374666):​n.407G>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 0.621 in 151,934 control chromosomes in the GnomAD database, including 29,950 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 0.62 ( 29950 hom., cov: 31)

Consequence

LOC105374666
XR_001742615.2 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.97
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=-1.01).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC105374666XR_001742615.2 linkuse as main transcriptn.407G>A non_coding_transcript_exon_variant 3/3
LOC105374666XR_925809.3 linkuse as main transcriptn.305+2694G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC02223ENST00000511596.5 linkuse as main transcriptn.195+2694G>A intron_variant 5
LINC02223ENST00000648234.1 linkuse as main transcriptn.451+2694G>A intron_variant
LINC02223ENST00000650405.1 linkuse as main transcriptn.217+27665G>A intron_variant

Frequencies

GnomAD3 genomes
AF:
0.621
AC:
94254
AN:
151816
Hom.:
29939
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.474
Gnomad AMI
AF:
0.721
Gnomad AMR
AF:
0.609
Gnomad ASJ
AF:
0.733
Gnomad EAS
AF:
0.557
Gnomad SAS
AF:
0.633
Gnomad FIN
AF:
0.695
Gnomad MID
AF:
0.611
Gnomad NFE
AF:
0.697
Gnomad OTH
AF:
0.654
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.621
AC:
94300
AN:
151934
Hom.:
29950
Cov.:
31
AF XY:
0.619
AC XY:
45971
AN XY:
74232
show subpopulations
Gnomad4 AFR
AF:
0.474
Gnomad4 AMR
AF:
0.609
Gnomad4 ASJ
AF:
0.733
Gnomad4 EAS
AF:
0.558
Gnomad4 SAS
AF:
0.634
Gnomad4 FIN
AF:
0.695
Gnomad4 NFE
AF:
0.697
Gnomad4 OTH
AF:
0.656
Alfa
AF:
0.651
Hom.:
5193
Bravo
AF:
0.609
Asia WGS
AF:
0.574
AC:
1996
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
0.34
DANN
Benign
0.77

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: rs10805650; hg19: chr5-17771787; API