Variant 2-27444430-A-G 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_015662.3(IFT172):c.*2T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 1,597,070 control chromosomes in the GnomAD database, including 134,840 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.46 ( 17909 hom., cov: 31)

Exomes 𝑓: 0.39 ( 116931 hom. )

Consequence

IFT172
NM_015662.3 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.328

Variant links:

Genes affected

IFT172 (HGNC:30391): (intraflagellar transport 172) This gene encodes a subunit of the intraflagellar transport subcomplex IFT-B. Subcomplexes IFT-A and IFT-B are necessary for ciliary assembly and maintenance. Mutations in this gene have been associated with skeletal ciliopathies, with or without polydactyly, such as such short-rib thoracic dysplasias 1, 9 or 10. [provided by RefSeq, Mar 2014]

IFT172 links:

KRTCAP3 (HGNC:28943): (keratinocyte associated protein 3) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

KRTCAP3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 2-27444430-A-G is Benign according to our data. Variant chr2-27444430-A-G is described in ClinVar as [Benign]. Clinvar id is 379412.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFT172	NM_015662.3 link	c.*2T>C		3_prime_UTR_variant	Exon 48 of 48	ENST00000260570.8	NP_056477.1	Q9UG01-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFT172	ENST00000260570 link	c.*2T>C		3_prime_UTR_variant	Exon 48 of 48	1	NM_015662.3	ENSP00000260570.3		Q9UG01-1

Frequencies

GnomAD3 genomes

AF:

0.464

AC:

70447

AN:

151706

Hom.:

17865

Cov.:

show subpopulations

Gnomad AFR

AF:

0.667

Gnomad AMI

AF:

0.221

Gnomad AMR

AF:

0.473

Gnomad ASJ

AF:

0.334

Gnomad EAS

AF:

0.154

Gnomad SAS

AF:

0.424

Gnomad FIN

AF:

0.430

Gnomad MID

AF:

0.367

Gnomad NFE

AF:

0.383

Gnomad OTH

AF:

0.406

GnomAD3 exomes

AF:

0.415

AC:

102662

AN:

247210

Hom.:

23076

AF XY:

0.405

AC XY:

54041

AN XY:

133494

show subpopulations

Gnomad AFR exome

AF:

0.672

Gnomad AMR exome

AF:

0.562

Gnomad ASJ exome

AF:

0.339

Gnomad EAS exome

AF:

0.152

Gnomad SAS exome

AF:

0.421

Gnomad FIN exome

AF:

0.427

Gnomad NFE exome

AF:

0.381

Gnomad OTH exome

AF:

0.395

GnomAD4 exome

AF:

0.394

AC:

569943

AN:

1445246

Hom.:

116931

Cov.:

AF XY:

0.393

AC XY:

282650

AN XY:

719750

show subpopulations

Gnomad4 AFR exome

AF:

0.676

Gnomad4 AMR exome

AF:

0.556

Gnomad4 ASJ exome

AF:

0.339

Gnomad4 EAS exome

AF:

0.133

Gnomad4 SAS exome

AF:

0.418

Gnomad4 FIN exome

AF:

0.431

Gnomad4 NFE exome

AF:

0.387

Gnomad4 OTH exome

AF:

0.391

GnomAD4 genome

AF:

0.465

AC:

70554

AN:

151824

Hom.:

17909

Cov.:

AF XY:

0.463

AC XY:

34374

AN XY:

74184

show subpopulations

Gnomad4 AFR

AF:

0.667

Gnomad4 AMR

AF:

0.473

Gnomad4 ASJ

AF:

0.334

Gnomad4 EAS

AF:

0.154

Gnomad4 SAS

AF:

0.425

Gnomad4 FIN

AF:

0.430

Gnomad4 NFE

AF:

0.383

Gnomad4 OTH

AF:

0.409

Alfa

AF:

0.389

Hom.:

18199

Bravo

AF:

0.475

Asia WGS

AF:

0.358

AC:

1245

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Jan 08, 2016

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Retinal dystrophy

Benign:1

Oct 01, 2023

Dept Of Ophthalmology, Nagoya University

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: research

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.1

DANN

Benign

0.59

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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