13-20567683-A-G

Position:

• chr13-20567683-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000319980.10(IFT88):​c.-195A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0861 in 1,142,676 control chromosomes in the GnomAD database, including 5,674 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.093 (901 hom., cov: 33)
  • Exomes 𝑓: 0.085 (4773 hom.)
• Consequence: IFT88 ENST00000319980.10 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.134

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 13-20567683-A-G is Benign according to our data. Variant chr13-20567683-A-G is described in ClinVar as [Benign]. Clinvar id is 1257994.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IFT88	NM_006531.5	c.-7+427A>G		intron_variant		ENST00000351808.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IFT88	ENST00000319980.10	c.-195A>G		5_prime_UTR_variant	2/28	1
IFT88	ENST00000351808.10	c.-7+427A>G		intron_variant		1	NM_006531.5	P1
IFT88	ENST00000389373.3	c.-321A>G		5_prime_UTR_variant	2/4	4

Frequencies

GnomAD3 genomes AF: 0.0928 AC: 14116 AN: 152166 Hom.: 903 Cov.: 33

Gnomad AFR AF: 0.0874

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.0936

Gnomad ASJ AF: 0.0479

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0904

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0733

Gnomad OTH AF: 0.0827

GnomAD4 exome AF: 0.0851 AC: 84257 AN: 990392 Hom.: 4773 Cov.: 16 AF XY: 0.0846 AC XY: 39490 AN XY: 466742

Gnomad4 AFR exome AF: 0.0838

Gnomad4 AMR exome AF: 0.111

Gnomad4 ASJ exome AF: 0.0449

Gnomad4 EAS exome AF: 0.374

Gnomad4 SAS exome AF: 0.141

Gnomad4 FIN exome AF: 0.0802

Gnomad4 NFE exome AF: 0.0770

Gnomad4 OTH exome AF: 0.0998

GnomAD4 genome AF: 0.0927 AC: 14112 AN: 152284 Hom.: 901 Cov.: 33 AF XY: 0.0959 AC XY: 7144 AN XY: 74468

Gnomad4 AFR AF: 0.0872

Gnomad4 AMR AF: 0.0935

Gnomad4 ASJ AF: 0.0479

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.0904

Gnomad4 NFE AF: 0.0733

Gnomad4 OTH AF: 0.0833

Alfa AF: 0.0574 Hom.: 80

Bravo AF: 0.0934

Asia WGS AF: 0.255 AC: 886 AN: 3478

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

GeneDx

Jun 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.0
DANN	Benign	0.75

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs9552244; hg19: chr13-21141822;