chr14-76007547-G-T

Position:

• chr14-76007547-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001102564.3(IFT43):​c.148-14780G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.854 in 152,088 control chromosomes in the GnomAD database, including 55,722 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.85 (55722 hom., cov: 32)
• Consequence: IFT43 NM_001102564.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.05

Genes affected

IFT43 (HGNC:29669): (intraflagellar transport 43) This gene encodes a subunit of the intraflagellar transport complex A (IFT-A). IFT-A is a multiprotein complex that plays an important role in cilia assembly and maintenance by mediating retrograde ciliary transport. Mutations in this gene are a cause of cranioectodermal dysplasia-3 (CED3), also known as Sensenbrenner syndrome. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]

IFT43 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IFT43	NM_001102564.3	c.148-14780G>T		intron_variant		ENST00000314067.11	NP_001096034.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFT43	ENST00000314067.11	c.148-14780G>T		intron_variant		2	NM_001102564.3	ENSP00000324177.6

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129813 AN: 151970 Hom.: 55680 Cov.: 32

Gnomad AFR AF: 0.907

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.760

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.843

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.854 AC: 129914 AN: 152088 Hom.: 55722 Cov.: 32 AF XY: 0.849 AC XY: 63137 AN XY: 74332

Gnomad4 AFR AF: 0.907

Gnomad4 AMR AF: 0.813

Gnomad4 ASJ AF: 0.808

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.816

Gnomad4 FIN AF: 0.840

Gnomad4 NFE AF: 0.853

Gnomad4 OTH AF: 0.838

Alfa AF: 0.854 Hom.: 6495

Bravo AF: 0.857

Asia WGS AF: 0.757 AC: 2632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	19
DANN	Benign	0.68

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

Other links and lift over

dbSNP: rs7149264; hg19: chr14-76473890;