Menu
GeneBe

rs17660212

chr16-2868291-A-G

Variant summary

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

The 16-2868291-A-G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,214 control chromosomes in the GnomAD database, including 6,925 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 0.26 ( 6925 hom., cov: 34)

Consequence


ENST00000662388.1 upstream_gene

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.07
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=-0.99).
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 = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000662388.1 linkuse as main transcript upstream_gene_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.265
AC:
40327
AN:
152096
Hom.:
6927
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.0805
Gnomad AMI
AF:
0.286
Gnomad AMR
AF:
0.274
Gnomad ASJ
AF:
0.423
Gnomad EAS
AF:
0.00270
Gnomad SAS
AF:
0.0988
Gnomad FIN
AF:
0.297
Gnomad MID
AF:
0.377
Gnomad NFE
AF:
0.392
Gnomad OTH
AF:
0.337
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:
0.265
AC:
40313
AN:
152214
Hom.:
6925
Cov.:
34
AF XY:
0.256
AC XY:
19014
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.0803
Gnomad4 AMR
AF:
0.273
Gnomad4 ASJ
AF:
0.423
Gnomad4 EAS
AF:
0.00270
Gnomad4 SAS
AF:
0.0998
Gnomad4 FIN
AF:
0.297
Gnomad4 NFE
AF:
0.391
Gnomad4 OTH
AF:
0.334
Alfa
AF:
0.346
Hom.:
4671
Bravo
AF:
0.258
Asia WGS
AF:
0.0570
AC:
199
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
Cadd
Benign
0.42
Dann
Benign
0.25

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: rs17660212; hg19: chr16-2918292; API