GeneBe

15-39688081-C-G

Variant names:

Variant summary

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

The NM_152597.5(FSIP1):​c.1188+25363G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 152,124 control chromosomes in the GnomAD database, including 51,784 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 0.82 ( 51784 hom., cov: 31)

Consequence

FSIP1
NM_152597.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.57

Publications

4 publications found
Variant links:
Genes affected
FSIP1 (HGNC:21674): (fibrous sheath interacting protein 1)

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=-0.93).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FSIP1NM_152597.5 linkc.1188+25363G>C intron_variant Intron 10 of 11 ENST00000350221.4 NP_689810.3 Q8NA03A0A024R9J2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FSIP1ENST00000350221.4 linkc.1188+25363G>C intron_variant Intron 10 of 11 1 NM_152597.5 ENSP00000280236.3 Q8NA03

Frequencies

GnomAD3 genomes
AF:
0.820
AC:
124594
AN:
152006
Hom.:
51739
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.702
Gnomad AMI
AF:
0.899
Gnomad AMR
AF:
0.830
Gnomad ASJ
AF:
0.821
Gnomad EAS
AF:
0.603
Gnomad SAS
AF:
0.834
Gnomad FIN
AF:
0.907
Gnomad MID
AF:
0.775
Gnomad NFE
AF:
0.890
Gnomad OTH
AF:
0.813
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.820
AC:
124699
AN:
152124
Hom.:
51784
Cov.:
31
AF XY:
0.823
AC XY:
61225
AN XY:
74370
show subpopulations
African (AFR)
AF:
0.702
AC:
29138
AN:
41480
American (AMR)
AF:
0.830
AC:
12692
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
0.821
AC:
2852
AN:
3472
East Asian (EAS)
AF:
0.602
AC:
3112
AN:
5166
South Asian (SAS)
AF:
0.834
AC:
4019
AN:
4818
European-Finnish (FIN)
AF:
0.907
AC:
9611
AN:
10596
Middle Eastern (MID)
AF:
0.776
AC:
228
AN:
294
European-Non Finnish (NFE)
AF:
0.890
AC:
60514
AN:
67992
Other (OTH)
AF:
0.813
AC:
1715
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1084
2167
3251
4334
5418
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
880
1760
2640
3520
4400
<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:
0.861
Hom.:
3312
Bravo
AF:
0.805
Asia WGS
AF:
0.756
AC:
2629
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.18
DANN
Benign
0.70
PhyloP100
-1.6
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: rs2664124; hg19: chr15-39980282; API