Variant chr13-20568002-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The ENST00000319980.10(IFT88):c.21+5C>T variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00114 in 713,254 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00082 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0012 ( 3 hom. )

Consequence

IFT88
ENST00000319980.10 splice_donor_5th_base, intron

Scores

Splicing: ADA: 0.001220

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0570

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 13-20568002-C-T is Benign according to our data. Variant chr13-20568002-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1585380.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IFT88	NM_006531.5 linkuse as main transcript	c.-7+746C>T		intron_variant		ENST00000351808.10

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
IFT88	ENST00000351808.10 linkuse as main transcript	c.-7+746C>T	intron_variant	1	NM_006531.5	P1	Q13099-2
IFT88	ENST00000319980.10 linkuse as main transcript	c.21+5C>T	splice_donor_5th_base_variant, intron_variant	1			Q13099-1
IFT88	ENST00000389373.3 linkuse as main transcript	c.-7+5C>T	splice_donor_5th_base_variant, intron_variant	4

Frequencies

GnomAD3 genomes

AF:

0.000825

AC:

125

AN:

151534

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000146

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000263

Gnomad ASJ

AF:

0.00288

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.000415

Gnomad FIN

AF:

0.000385

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00141

Gnomad OTH

AF:

0.000956

GnomAD3 exomes

AF:

0.00101

AC:

150

AN:

149048

Hom.:

AF XY:

0.000899

AC XY:

AN XY:

78934

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000405

Gnomad ASJ exome

AF:

0.00353

Gnomad EAS exome

AF:

0.0000897

Gnomad SAS exome

AF:

0.000132

Gnomad FIN exome

AF:

0.000351

Gnomad NFE exome

AF:

0.00163

Gnomad OTH exome

AF:

0.00183

GnomAD4 exome

AF:

0.00123

AC:

690

AN:

561612

Hom.:

Cov.:

AF XY:

0.00129

AC XY:

391

AN XY:

303370

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.000375

Gnomad4 ASJ exome

AF:

0.00375

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000223

Gnomad4 FIN exome

AF:

0.000357

Gnomad4 NFE exome

AF:

0.00167

Gnomad4 OTH exome

AF:

0.00108

GnomAD4 genome

AF:

0.000824

AC:

125

AN:

151642

Hom.:

Cov.:

AF XY:

0.000675

AC XY:

AN XY:

74070

show subpopulations

Gnomad4 AFR

AF:

0.000145

Gnomad4 AMR

AF:

0.000263

Gnomad4 ASJ

AF:

0.00288

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.000415

Gnomad4 FIN

AF:

0.000385

Gnomad4 NFE

AF:

0.00141

Gnomad4 OTH

AF:

0.000946

Alfa

AF:

0.00131

Hom.:

Bravo

AF:

0.000876

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Jan 20, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.5

DANN

Benign

0.37

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.0012

dbscSNV1_RF

Benign

0.036

SpliceAI score (max)

0.050

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