GeneBe

rs2065914

Positions:

Variant summary

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

The 1-240007496-T-C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,778 control chromosomes in the GnomAD database, including 11,754 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 0.39 ( 11754 hom., cov: 31)

Consequence

RPS7P5
NR_036695.2 upstream_gene

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.288
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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RPS7P5NR_036695.2 linkuse as main transcript upstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000668221.1 linkuse as main transcript upstream_gene_variant

Frequencies

GnomAD3 genomes
AF:
0.387
AC:
58736
AN:
151660
Hom.:
11755
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.338
Gnomad AMI
AF:
0.378
Gnomad AMR
AF:
0.318
Gnomad ASJ
AF:
0.483
Gnomad EAS
AF:
0.207
Gnomad SAS
AF:
0.372
Gnomad FIN
AF:
0.410
Gnomad MID
AF:
0.405
Gnomad NFE
AF:
0.439
Gnomad OTH
AF:
0.392
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.387
AC:
58746
AN:
151778
Hom.:
11754
Cov.:
31
AF XY:
0.385
AC XY:
28577
AN XY:
74152
show subpopulations
Gnomad4 AFR
AF:
0.338
Gnomad4 AMR
AF:
0.318
Gnomad4 ASJ
AF:
0.483
Gnomad4 EAS
AF:
0.206
Gnomad4 SAS
AF:
0.373
Gnomad4 FIN
AF:
0.410
Gnomad4 NFE
AF:
0.439
Gnomad4 OTH
AF:
0.390
Alfa
AF:
0.420
Hom.:
18738
Bravo
AF:
0.375
Asia WGS
AF:
0.277
AC:
967
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
2.2
DANN
Benign
0.52

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: rs2065914; hg19: chr1-240170796; API