20-43637268-CTT-CTTT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_016004.5(IFT52):​c.1120+26dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0396 in 1,128,950 control chromosomes in the GnomAD database, including 11 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0021 ( 3 hom., cov: 33)
Exomes 𝑓: 0.045 ( 8 hom. )

Consequence

IFT52
NM_016004.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0880
Variant links:
Genes affected
IFT52 (HGNC:15901): (intraflagellar transport 52) This gene encodes a conserved proline-rich protein that is a component of the intraflagellar transport-B (IFT-B) core complex. The encoded protein is essential for the integrity of the IFT-B core complex, and for biosynthesis and maintenance of cilia. Mutations in this gene are associated with ciliopathy that affects the skeleton. [provided by RefSeq, Oct 2016]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 20-43637268-C-CT is Benign according to our data. Variant chr20-43637268-C-CT is described in ClinVar as [Benign]. Clinvar id is 1614780.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.0452 (44375/981104) while in subpopulation EAS AF= 0.051 (1388/27220). AF 95% confidence interval is 0.0488. There are 8 homozygotes in gnomad4_exome. There are 22063 alleles in male gnomad4_exome subpopulation. Median coverage is 15. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
IFT52NM_016004.5 linkc.1120+26dupT intron_variant ENST00000373030.8 NP_057088.2 Q9Y366

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
IFT52ENST00000373030.8 linkc.1120+15_1120+16insT intron_variant 1 NM_016004.5 ENSP00000362121.3 Q9Y366
IFT52ENST00000373039.4 linkc.1120+15_1120+16insT intron_variant 5 ENSP00000362130.4 Q9Y366
IFT52ENST00000461012.1 linkn.107+15_107+16insT intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.00209
AC:
309
AN:
147778
Hom.:
3
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000123
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000272
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000392
Gnomad SAS
AF:
0.000213
Gnomad FIN
AF:
0.0250
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000797
Gnomad OTH
AF:
0.00198
GnomAD4 exome
AF:
0.0452
AC:
44375
AN:
981104
Hom.:
8
Cov.:
15
AF XY:
0.0456
AC XY:
22063
AN XY:
484220
show subpopulations
Gnomad4 AFR exome
AF:
0.0434
Gnomad4 AMR exome
AF:
0.0436
Gnomad4 ASJ exome
AF:
0.0510
Gnomad4 EAS exome
AF:
0.0510
Gnomad4 SAS exome
AF:
0.0459
Gnomad4 FIN exome
AF:
0.0645
Gnomad4 NFE exome
AF:
0.0439
Gnomad4 OTH exome
AF:
0.0486
GnomAD4 genome
AF:
0.00209
AC:
309
AN:
147846
Hom.:
3
Cov.:
33
AF XY:
0.00315
AC XY:
227
AN XY:
72038
show subpopulations
Gnomad4 AFR
AF:
0.000123
Gnomad4 AMR
AF:
0.000271
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000393
Gnomad4 SAS
AF:
0.000214
Gnomad4 FIN
AF:
0.0250
Gnomad4 NFE
AF:
0.000797
Gnomad4 OTH
AF:
0.00196

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 18, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs754046046; hg19: chr20-42265908; API