20-43637268-CTT-CTTT

Position:

• chr20-43637268-CTT-CTTT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0880

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]

ACMG classification

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
IFT52	NM_016004.5	c.1120+26dupT		intron_variant		ENST00000373030.8	NP_057088.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFT52	ENST00000373030.8	c.1120+15_1120+16insT		intron_variant		1	NM_016004.5	ENSP00000362121.3
IFT52	ENST00000373039.4	c.1120+15_1120+16insT		intron_variant		5		ENSP00000362130.4
IFT52	ENST00000461012.1	n.107+15_107+16insT		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.00209 AC: 309 AN: 147778 Hom.: 3 Cov.: 33

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

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

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

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 18, 2024

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs754046046; hg19: chr20-42265908;