chr2-29160508-G-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_024692.6(CLIP4):​c.1534+41G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000688 in 1,454,192 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

CLIP4
NM_024692.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.102

Publications

0 publications found
Variant links:
Genes affected
CLIP4 (HGNC:26108): (CAP-Gly domain containing linker protein family member 4) Predicted to enable microtubule plus-end binding activity. Predicted to be involved in cytoplasmic microtubule organization. Located in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CLIP4NM_024692.6 linkc.1534+41G>C intron_variant Intron 12 of 15 ENST00000320081.10 NP_078968.3 Q8N3C7-1B7Z936

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CLIP4ENST00000320081.10 linkc.1534+41G>C intron_variant Intron 12 of 15 1 NM_024692.6 ENSP00000327009.5 Q8N3C7-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.88e-7
AC:
1
AN:
1454192
Hom.:
0
Cov.:
30
AF XY:
0.00000138
AC XY:
1
AN XY:
722740
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
33118
American (AMR)
AF:
0.00
AC:
0
AN:
43684
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25798
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39594
South Asian (SAS)
AF:
0.0000118
AC:
1
AN:
84708
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53318
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5706
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1108210
Other (OTH)
AF:
0.00
AC:
0
AN:
60056
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.19
DANN
Benign
0.25
PhyloP100
-0.10

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: rs2305450; hg19: chr2-29383374; API