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17-69362956-C-T

Variant summary

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

The 17-69362956-C-T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,200 control chromosomes in the GnomAD database, including 1,126 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 0.11 ( 1126 hom., cov: 32)

Consequence

LOC105371879
XR_934950.3 upstream_gene

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00600
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
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105371879XR_934950.3 linkuse as main transcript upstream_gene_variant

Ensembl

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

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.105
AC:
16009
AN:
152082
Hom.:
1125
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0316
Gnomad AMI
AF:
0.103
Gnomad AMR
AF:
0.106
Gnomad ASJ
AF:
0.119
Gnomad EAS
AF:
0.000578
Gnomad SAS
AF:
0.0509
Gnomad FIN
AF:
0.120
Gnomad MID
AF:
0.0918
Gnomad NFE
AF:
0.159
Gnomad OTH
AF:
0.104
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.105
AC:
16012
AN:
152200
Hom.:
1126
Cov.:
32
AF XY:
0.102
AC XY:
7625
AN XY:
74406
show subpopulations
Gnomad4 AFR
AF:
0.0315
Gnomad4 AMR
AF:
0.106
Gnomad4 ASJ
AF:
0.119
Gnomad4 EAS
AF:
0.000580
Gnomad4 SAS
AF:
0.0511
Gnomad4 FIN
AF:
0.120
Gnomad4 NFE
AF:
0.159
Gnomad4 OTH
AF:
0.103
Alfa
AF:
0.126
Hom.:
941
Bravo
AF:
0.101
Asia WGS
AF:
0.0330
AC:
113
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
6.4
Dann
Benign
0.64

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: rs560271; hg19: chr17-67359097; API