GeneBe

17-44364976-T-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.393 in 692,192 control chromosomes in the GnomAD database, including 54,036 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 ( 11891 hom., cov: 31)
Exomes 𝑓: 0.39 ( 42145 hom. )

Consequence

RPL7L1P5
intragenic

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.226

Publications

36 publications found
Variant links:
Genes affected
RPL7L1P5 (HGNC:39487): (RPL7L1 pseudogene 5)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RPL7L1P5 n.44364976T>C intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RPL7L1P5ENST00000590816.1 linkn.*38A>G downstream_gene_variant 6

Frequencies

GnomAD3 genomes
AF:
0.395
AC:
59975
AN:
151752
Hom.:
11896
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.391
Gnomad AMI
AF:
0.413
Gnomad AMR
AF:
0.360
Gnomad ASJ
AF:
0.450
Gnomad EAS
AF:
0.447
Gnomad SAS
AF:
0.355
Gnomad FIN
AF:
0.439
Gnomad MID
AF:
0.323
Gnomad NFE
AF:
0.396
Gnomad OTH
AF:
0.370
GnomAD4 exome
AF:
0.392
AC:
212054
AN:
540322
Hom.:
42145
Cov.:
6
AF XY:
0.390
AC XY:
113019
AN XY:
289802
show subpopulations
African (AFR)
AF:
0.380
AC:
5565
AN:
14664
American (AMR)
AF:
0.389
AC:
10923
AN:
28100
Ashkenazi Jewish (ASJ)
AF:
0.440
AC:
8113
AN:
18418
East Asian (EAS)
AF:
0.432
AC:
13329
AN:
30870
South Asian (SAS)
AF:
0.351
AC:
20707
AN:
59000
European-Finnish (FIN)
AF:
0.435
AC:
13614
AN:
31294
Middle Eastern (MID)
AF:
0.346
AC:
797
AN:
2302
European-Non Finnish (NFE)
AF:
0.391
AC:
127616
AN:
326514
Other (OTH)
AF:
0.391
AC:
11390
AN:
29160
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.510
Heterozygous variant carriers
0
5892
11784
17675
23567
29459
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
1112
2224
3336
4448
5560
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.395
AC:
59981
AN:
151870
Hom.:
11891
Cov.:
31
AF XY:
0.393
AC XY:
29134
AN XY:
74188
show subpopulations
African (AFR)
AF:
0.390
AC:
16170
AN:
41414
American (AMR)
AF:
0.360
AC:
5489
AN:
15258
Ashkenazi Jewish (ASJ)
AF:
0.450
AC:
1560
AN:
3468
East Asian (EAS)
AF:
0.446
AC:
2310
AN:
5174
South Asian (SAS)
AF:
0.353
AC:
1699
AN:
4812
European-Finnish (FIN)
AF:
0.439
AC:
4610
AN:
10512
Middle Eastern (MID)
AF:
0.323
AC:
95
AN:
294
European-Non Finnish (NFE)
AF:
0.396
AC:
26900
AN:
67924
Other (OTH)
AF:
0.367
AC:
772
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1888
3777
5665
7554
9442
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
578
1156
1734
2312
2890
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.393
Hom.:
48045
Bravo
AF:
0.389
Asia WGS
AF:
0.405
AC:
1416
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.64
CADD
Benign
5.3
DANN
Benign
0.59
PhyloP100
-0.23

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs708382; hg19: chr17-42442344; API