Variant 13-20631001-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006531.5(IFT88):c.1300-15A>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 1,462,846 control chromosomes in the GnomAD database, including 400,386 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.70 ( 37816 hom., cov: 31)

Exomes 𝑓: 0.74 ( 362570 hom. )

Consequence

IFT88
NM_006531.5 splice_polypyrimidine_tract, intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.109

Variant links:

Genes affected

IFT88 (HGNC:20606): (intraflagellar transport 88) This gene encodes a member of the tetratrico peptide repeat (TPR) family. The encoded protein is involved in cilium biogenesis. Mutations of a similar gene in mouse can cause polycystic kidney disease. Several transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2017]

IFT88 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 13-20631001-A-T is Benign according to our data. Variant chr13-20631001-A-T is described in ClinVar as [Benign]. Clinvar id is 402966.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-20631001-A-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IFT88	NM_006531.5 linkuse as main transcript	c.1300-15A>T		splice_polypyrimidine_tract_variant, intron_variant		ENST00000351808.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IFT88	ENST00000351808.10 linkuse as main transcript	c.1300-15A>T		splice_polypyrimidine_tract_variant, intron_variant		1	NM_006531.5	P1	Q13099-2

Frequencies

GnomAD3 genomes

AF:

0.696

AC:

105641

AN:

151826

Hom.:

37800

Cov.:

show subpopulations

Gnomad AFR

AF:

0.540

Gnomad AMI

AF:

0.749

Gnomad AMR

AF:

0.778

Gnomad ASJ

AF:

0.687

Gnomad EAS

AF:

0.996

Gnomad SAS

AF:

0.885

Gnomad FIN

AF:

0.746

Gnomad MID

AF:

0.725

Gnomad NFE

AF:

0.726

Gnomad OTH

AF:

0.718

GnomAD3 exomes

AF:

0.770

AC:

192903

AN:

250504

Hom.:

75893

AF XY:

0.774

AC XY:

104886

AN XY:

135436

show subpopulations

Gnomad AFR exome

AF:

0.531

Gnomad AMR exome

AF:

0.854

Gnomad ASJ exome

AF:

0.694

Gnomad EAS exome

AF:

0.997

Gnomad SAS exome

AF:

0.878

Gnomad FIN exome

AF:

0.748

Gnomad NFE exome

AF:

0.725

Gnomad OTH exome

AF:

0.740

GnomAD4 exome

AF:

0.740

AC:

969548

AN:

1310902

Hom.:

362570

Cov.:

AF XY:

0.745

AC XY:

492163

AN XY:

660512

show subpopulations

Gnomad4 AFR exome

AF:

0.519

Gnomad4 AMR exome

AF:

0.843

Gnomad4 ASJ exome

AF:

0.683

Gnomad4 EAS exome

AF:

0.998

Gnomad4 SAS exome

AF:

0.871

Gnomad4 FIN exome

AF:

0.745

Gnomad4 NFE exome

AF:

0.722

Gnomad4 OTH exome

AF:

0.735

GnomAD4 genome

AF:

0.696

AC:

105703

AN:

151944

Hom.:

37816

Cov.:

AF XY:

0.705

AC XY:

52309

AN XY:

74240

show subpopulations

Gnomad4 AFR

AF:

0.540

Gnomad4 AMR

AF:

0.779

Gnomad4 ASJ

AF:

0.687

Gnomad4 EAS

AF:

0.996

Gnomad4 SAS

AF:

0.885

Gnomad4 FIN

AF:

0.746

Gnomad4 NFE

AF:

0.726

Gnomad4 OTH

AF:

0.719

Alfa

AF:

0.672

Hom.:

4398

Bravo

AF:

0.688

Asia WGS

AF:

0.915

AC:

3179

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

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

Invitae

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

7.4

DANN

Benign

0.79

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over