chr5-10463995-C-T

Variant summary

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

The NM_031916.5(ROPN1L):​c.594-853C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,144 control chromosomes in the GnomAD database, including 4,011 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 0.19 ( 4011 hom., cov: 33)

Consequence

ROPN1L
NM_031916.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.11

Publications

21 publications found
Variant links:
Genes affected
ROPN1L (HGNC:24060): (rhophilin associated tail protein 1 like) This gene encodes a member of the ropporin family. The encoded protein is present in sperm and interacts with A-kinase anchoring protein, AKAP3, through the amphipathic helix region of AKAP3. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Oct 2014]

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=-0.96).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ROPN1LNM_031916.5 linkc.594-853C>T intron_variant Intron 4 of 4 ENST00000274134.5 NP_114122.2 Q96C74

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ROPN1LENST00000274134.5 linkc.594-853C>T intron_variant Intron 4 of 4 1 NM_031916.5 ENSP00000274134.4 Q96C74

Frequencies

GnomAD3 genomes
AF:
0.192
AC:
29226
AN:
152026
Hom.:
3987
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.245
Gnomad AMI
AF:
0.127
Gnomad AMR
AF:
0.308
Gnomad ASJ
AF:
0.154
Gnomad EAS
AF:
0.661
Gnomad SAS
AF:
0.308
Gnomad FIN
AF:
0.112
Gnomad MID
AF:
0.104
Gnomad NFE
AF:
0.106
Gnomad OTH
AF:
0.183
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.193
AC:
29295
AN:
152144
Hom.:
4011
Cov.:
33
AF XY:
0.200
AC XY:
14867
AN XY:
74388
show subpopulations
African (AFR)
AF:
0.245
AC:
10188
AN:
41506
American (AMR)
AF:
0.309
AC:
4717
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
0.154
AC:
535
AN:
3472
East Asian (EAS)
AF:
0.660
AC:
3388
AN:
5130
South Asian (SAS)
AF:
0.310
AC:
1493
AN:
4822
European-Finnish (FIN)
AF:
0.112
AC:
1194
AN:
10614
Middle Eastern (MID)
AF:
0.105
AC:
31
AN:
294
European-Non Finnish (NFE)
AF:
0.106
AC:
7234
AN:
67994
Other (OTH)
AF:
0.189
AC:
399
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1062
2124
3186
4248
5310
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
304
608
912
1216
1520
<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:
0.145
Hom.:
8223
Bravo
AF:
0.212
Asia WGS
AF:
0.508
AC:
1765
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.20
DANN
Benign
0.54
PhyloP100
-2.1
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs2967951; hg19: chr5-10464107; API