2-27444951-G-GT

Variant summary

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

The NM_015662.3(IFT172):c.5160+62_5160+63insA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0105 in 1,481,986 control chromosomes in the GnomAD database, including 630 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.040 (362 hom., cov: 32)
  • Exomes 𝑓: 0.0072 (268 hom.)
• Consequence: IFT172 NM_015662.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.217

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 2-27444951-G-GT is Benign according to our data. Variant chr2-27444951-G-GT is described in ClinVar as [Benign]. Clinvar id is 1248200.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IFT172	NM_015662.3	c.5160+62_5160+63insA		intron_variant		ENST00000260570.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IFT172	ENST00000260570.8	c.5160+62_5160+63insA		intron_variant		1	NM_015662.3	P1

Frequencies

GnomAD3 genomes AF: 0.0394 AC: 5941 AN: 150846 Hom.: 358 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0153

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000629

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00955

Gnomad NFE AF: 0.000429

Gnomad OTH AF: 0.0257

GnomAD4 exome AF: 0.00718 AC: 9558 AN: 1331022 Hom.: 268 AF XY: 0.00672 AC XY: 4456 AN XY: 663048

Gnomad4 AFR exome AF: 0.148

Gnomad4 AMR exome AF: 0.00949

Gnomad4 ASJ exome AF: 0.00259

Gnomad4 EAS exome AF: 0.00182

Gnomad4 SAS exome AF: 0.00283

Gnomad4 FIN exome AF: 0.00255

Gnomad4 NFE exome AF: 0.00354

Gnomad4 OTH exome AF: 0.0126

GnomAD4 genome AF: 0.0396 AC: 5975 AN: 150964 Hom.: 362 Cov.: 32 AF XY: 0.0392 AC XY: 2892 AN XY: 73780

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.0152

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000420

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000429

Gnomad4 OTH AF: 0.0259

Bravo AF: 0.0451

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

Aug 06, 2019

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Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs111756175; hg19: chr2-27667818;