chr20-43637268-CT-C

Position:

• chr20-43637268-CT-C

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_Strong BA1

The NM_016004.5(IFT52):​c.1120+26delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.037 in 1,108,334 control chromosomes in the GnomAD database, including 29 homozygotes. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0078 (15 hom., cov: 33)
  • Exomes 𝑓: 0.041 (14 hom.)
• Consequence: IFT52 NM_016004.5 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• 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]

IFT52 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -16 ACMG points.

• BP6: Variant 20-43637268-CT-C is Benign according to our data. Variant chr20-43637268-CT-C is described in ClinVar as [Benign]. Clinvar id is 402964.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IFT52	NM_016004.5	c.1120+26delT		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+26delT		intron_variant		1	NM_016004.5	ENSP00000362121.3
IFT52	ENST00000373039.4	c.1120+26delT		intron_variant		5		ENSP00000362130.4
IFT52	ENST00000461012.1	n.107+26delT		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.00778 AC: 1149 AN: 147668 Hom.: 15 Cov.: 33

Gnomad AFR AF: 0.0256

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00380

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000196

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000942

Gnomad MID AF: 0.0132

Gnomad NFE AF: 0.000316

Gnomad OTH AF: 0.00988

GnomAD4 exome AF: 0.0415 AC: 39864 AN: 960600 Hom.: 14 Cov.: 15 AF XY: 0.0417 AC XY: 19786 AN XY: 473950

Gnomad4 AFR exome AF: 0.0724

Gnomad4 AMR exome AF: 0.0521

Gnomad4 ASJ exome AF: 0.0525

Gnomad4 EAS exome AF: 0.0539

Gnomad4 SAS exome AF: 0.0509

Gnomad4 FIN exome AF: 0.0412

Gnomad4 NFE exome AF: 0.0389

Gnomad4 OTH exome AF: 0.0467

GnomAD4 genome AF: 0.00780 AC: 1152 AN: 147734 Hom.: 15 Cov.: 33 AF XY: 0.00757 AC XY: 545 AN XY: 71974

Gnomad4 AFR AF: 0.0257

Gnomad4 AMR AF: 0.00380

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000197

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000942

Gnomad4 NFE AF: 0.000316

Gnomad4 OTH AF: 0.00978

Bravo AF: 0.00836

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 25, 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;