10-58503165-C-T

Variant summary

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

The XR_945981.3(LOC105378316):​n.874C>T 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 0.478 in 151,956 control chromosomes in the GnomAD database, including 17,627 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 0.48 ( 17627 hom., cov: 32)

Consequence

LOC105378316
XR_945981.3 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.552
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=-0.95).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC105378316XR_945981.3 linkuse as main transcriptn.874C>T non_coding_transcript_exon_variant 6/6

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.478
AC:
72556
AN:
151838
Hom.:
17601
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.543
Gnomad AMI
AF:
0.288
Gnomad AMR
AF:
0.487
Gnomad ASJ
AF:
0.397
Gnomad EAS
AF:
0.576
Gnomad SAS
AF:
0.601
Gnomad FIN
AF:
0.460
Gnomad MID
AF:
0.433
Gnomad NFE
AF:
0.430
Gnomad OTH
AF:
0.461
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.478
AC:
72629
AN:
151956
Hom.:
17627
Cov.:
32
AF XY:
0.483
AC XY:
35881
AN XY:
74278
show subpopulations
Gnomad4 AFR
AF:
0.543
Gnomad4 AMR
AF:
0.487
Gnomad4 ASJ
AF:
0.397
Gnomad4 EAS
AF:
0.576
Gnomad4 SAS
AF:
0.601
Gnomad4 FIN
AF:
0.460
Gnomad4 NFE
AF:
0.430
Gnomad4 OTH
AF:
0.466
Alfa
AF:
0.449
Hom.:
3120
Bravo
AF:
0.482
Asia WGS
AF:
0.594
AC:
2064
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.48
DANN
Benign
0.80

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: rs1427209; hg19: chr10-60262925; API