rs1983600

chr16-1528513-A-Cchr16-1528513-A-Gchr16-1528513-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014714.4(IFT140):c.2400-1717T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0668 in 150,846 control chromosomes in the GnomAD database, including 571 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 0.067 (571 hom., cov: 33)
• Consequence: IFT140 NM_014714.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

Genes affected

IFT140 (HGNC:29077): (intraflagellar transport 140) This gene encodes one of the subunits of the intraflagellar transport (IFT) complex A. Intraflagellar transport is involved in the genesis, resorption and signaling of primary cilia. The primary cilium is a microtubule-based sensory organelle at the surface of most quiescent mammalian cells, that receives signals from its environment, such as the flow of fluid, light or odors, and transduces those signals to the nucleus. Loss of the corresponding protein in mouse results in renal cystic disease. [provided by RefSeq, Jun 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IFT140	NM_014714.4	c.2400-1717T>G		intron_variant		ENST00000426508.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IFT140	ENST00000426508.7	c.2400-1717T>G		intron_variant		5	NM_014714.4	P1
IFT140	ENST00000361339.9	c.-19-1717T>G		intron_variant		1
IFT140	ENST00000397417.6	c.*952-1717T>G		intron_variant, NMD_transcript_variant		5
IFT140	ENST00000565298.5	n.1088-1717T>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0668 AC: 10074 AN: 150732 Hom.: 568 Cov.: 33

Gnomad AFR AF: 0.0210

Gnomad AMI AF: 0.0749

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.0388

Gnomad FIN AF: 0.0296

Gnomad MID AF: 0.0769

Gnomad NFE AF: 0.0672

Gnomad OTH AF: 0.0950

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

GnomAD4 genome AF: 0.0668 AC: 10079 AN: 150846 Hom.: 571 Cov.: 33 AF XY: 0.0672 AC XY: 4950 AN XY: 73664

Gnomad4 AFR AF: 0.0209

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.0388

Gnomad4 FIN AF: 0.0296

Gnomad4 NFE AF: 0.0672

Gnomad4 OTH AF: 0.0940

Alfa AF: 0.00191 Hom.: 0

Bravo AF: 0.0812

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.3
Dann	Benign	0.25

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: rs1983600; hg19: chr16-1578514; COSMIC: COSV54152982; COSMIC: COSV54152982;