Genetic Variant IFT172:c.2877+48T>G (chr2-27458731-A-C) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The NM_015662.3(IFT172):c.2877+48T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 1,598,526 control chromosomes in the GnomAD database, including 135,281 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.46 ( 17915 hom., cov: 32)

Exomes 𝑓: 0.40 ( 117366 hom. )

Consequence

IFT172
NM_015662.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -3.12

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:

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=-0.96).

BP6

Variant 2-27458731-A-C is Benign according to our data. Variant chr2-27458731-A-C is described in ClinVar as [Benign]. Clinvar id is 1257107.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFT172	NM_015662.3 link	c.2877+48T>G		intron_variant	Intron 26 of 47	ENST00000260570.8	NP_056477.1	Q9UG01-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFT172	ENST00000260570.8 link	c.2877+48T>G		intron_variant	Intron 26 of 47	1	NM_015662.3	ENSP00000260570.3		Q9UG01-1

Frequencies

GnomAD3 genomes

AF:

0.464

AC:

70509

AN:

151876

Hom.:

17871

Cov.:

show subpopulations

Gnomad AFR

AF:

0.667

Gnomad AMI

AF:

0.221

Gnomad AMR

AF:

0.473

Gnomad ASJ

AF:

0.335

Gnomad EAS

AF:

0.154

Gnomad SAS

AF:

0.424

Gnomad FIN

AF:

0.429

Gnomad MID

AF:

0.367

Gnomad NFE

AF:

0.383

Gnomad OTH

AF:

0.406

GnomAD3 exomes

AF:

0.418

AC:

100972

AN:

241592

Hom.:

22817

AF XY:

0.408

AC XY:

53253

AN XY:

130556

show subpopulations

Gnomad AFR exome

AF:

0.673

Gnomad AMR exome

AF:

0.567

Gnomad ASJ exome

AF:

0.340

Gnomad EAS exome

AF:

0.154

Gnomad SAS exome

AF:

0.423

Gnomad FIN exome

AF:

0.430

Gnomad NFE exome

AF:

0.384

Gnomad OTH exome

AF:

0.399

GnomAD4 exome

AF:

0.395

AC:

571988

AN:

1446532

Hom.:

117366

Cov.:

AF XY:

0.394

AC XY:

283507

AN XY:

719934

show subpopulations

Gnomad4 AFR exome

AF:

0.677

Gnomad4 AMR exome

AF:

0.558

Gnomad4 ASJ exome

AF:

0.339

Gnomad4 EAS exome

AF:

0.134

Gnomad4 SAS exome

AF:

0.418

Gnomad4 FIN exome

AF:

0.432

Gnomad4 NFE exome

AF:

0.388

Gnomad4 OTH exome

AF:

0.391

GnomAD4 genome

AF:

0.465

AC:

70615

AN:

151994

Hom.:

17915

Cov.:

AF XY:

0.463

AC XY:

34415

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.667

Gnomad4 AMR

AF:

0.474

Gnomad4 ASJ

AF:

0.335

Gnomad4 EAS

AF:

0.155

Gnomad4 SAS

AF:

0.424

Gnomad4 FIN

AF:

0.429

Gnomad4 NFE

AF:

0.383

Gnomad4 OTH

AF:

0.410

Alfa

AF:

0.373

Hom.:

6315

Bravo

AF:

0.475

Asia WGS

AF:

0.358

AC:

1244

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 26, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Short-rib thoracic dysplasia 10 with or without polydactyly

Benign:1

Aug 10, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Retinitis pigmentosa 71

Benign:1

Aug 10, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.18

DANN

Benign

0.33

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