2-27444653-T-TTTTG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_015662.3(IFT172):c.5161-133_5161-132insCAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 674,504 control chromosomes in the GnomAD database, including 77,134 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.55 (26429 hom., cov: 0)
  • Exomes 𝑓: 0.42 (50705 hom.)
• Consequence: IFT172 NM_015662.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.13

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]

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 2-27444653-T-TTTTG is Benign according to our data. Variant chr2-27444653-T-TTTTG is described in ClinVar as [Benign]. Clinvar id is 1268593.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IFT172	NM_015662.3	c.5161-133_5161-132insCAAA		intron_variant		ENST00000260570.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IFT172	ENST00000260570.8	c.5161-133_5161-132insCAAA		intron_variant		1	NM_015662.3	P1

Frequencies

GnomAD3 genomes AF: 0.554 AC: 83877 AN: 151282 Hom.: 26352 Cov.: 0

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.489

GnomAD4 exome AF: 0.417 AC: 218338 AN: 523102 Hom.: 50705 AF XY: 0.417 AC XY: 115082 AN XY: 275710

Gnomad4 AFR exome AF: 0.861

Gnomad4 AMR exome AF: 0.560

Gnomad4 ASJ exome AF: 0.352

Gnomad4 EAS exome AF: 0.127

Gnomad4 SAS exome AF: 0.473

Gnomad4 FIN exome AF: 0.459

Gnomad4 NFE exome AF: 0.406

Gnomad4 OTH exome AF: 0.440

GnomAD4 genome AF: 0.555 AC: 84027 AN: 151402 Hom.: 26429 Cov.: 0 AF XY: 0.549 AC XY: 40638 AN XY: 73972

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.493

Alfa AF: 0.317 Hom.: 651

Asia WGS AF: 0.390 AC: 1356 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 26, 2018

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10635082; hg19: chr2-27667520;