rs13193677

Variant summary

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

The NM_001130700.2(IPCEF1):​c.-61-8044C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0954 in 152,130 control chromosomes in the GnomAD database, including 796 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 0.095 ( 796 hom., cov: 32)

Consequence

IPCEF1
NM_001130700.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.370
Variant links:
Genes affected
IPCEF1 (HGNC:21204): (interaction protein for cytohesin exchange factors 1) Predicted to enable peroxidase activity. Predicted to be involved in response to oxidative stress. Predicted to be located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IPCEF1NM_001130700.2 linkuse as main transcriptc.-61-8044C>T intron_variant ENST00000367220.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IPCEF1ENST00000367220.9 linkuse as main transcriptc.-61-8044C>T intron_variant 2 NM_001130700.2 A2Q8WWN9-2
IPCEF1ENST00000265198.8 linkuse as main transcriptc.-61-8044C>T intron_variant 1 A2Q8WWN9-1
IPCEF1ENST00000422970.6 linkuse as main transcriptc.-61-8044C>T intron_variant 1 A2Q8WWN9-2
IPCEF1ENST00000520261.1 linkuse as main transcriptc.-61-8044C>T intron_variant 4

Frequencies

GnomAD3 genomes
AF:
0.0954
AC:
14509
AN:
152012
Hom.:
797
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.129
Gnomad AMI
AF:
0.0581
Gnomad AMR
AF:
0.0763
Gnomad ASJ
AF:
0.0845
Gnomad EAS
AF:
0.00135
Gnomad SAS
AF:
0.0443
Gnomad FIN
AF:
0.121
Gnomad MID
AF:
0.152
Gnomad NFE
AF:
0.0873
Gnomad OTH
AF:
0.0890
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0954
AC:
14507
AN:
152130
Hom.:
796
Cov.:
32
AF XY:
0.0955
AC XY:
7100
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.129
Gnomad4 AMR
AF:
0.0761
Gnomad4 ASJ
AF:
0.0845
Gnomad4 EAS
AF:
0.00135
Gnomad4 SAS
AF:
0.0439
Gnomad4 FIN
AF:
0.121
Gnomad4 NFE
AF:
0.0873
Gnomad4 OTH
AF:
0.0881
Alfa
AF:
0.0824
Hom.:
748
Bravo
AF:
0.0946
Asia WGS
AF:
0.0290
AC:
103
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
2.5
DANN
Benign
0.36

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs13193677; hg19: chr6-154618934; API