rs1983600

Variant names:

• chr16-1528513-A-C
• rs1983600
• NM_014714.4:c.2400-1717T>G

Your query was ambiguous. Multiple possible variants found:

• chr16-1528513-A-C
• chr16-1528513-A-G
• chr16-1528513-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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]

TMEM204 (HGNC:14158): (transmembrane protein 204) C16ORF30 plays a role in cell adhesion and cellular permeability at adherens junctions (Kearsey et al., 2004 [PubMed 15206924]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014714.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFT140	NM_014714.4	MANE Select	c.2400-1717T>G		intron	N/A	NP_055529.2
	TMEM204	NM_001256541.2		c.-626A>C		upstream_gene	N/A	NP_001243470.1	Q9BSN7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFT140	ENST00000426508.7	TSL:5 MANE Select	c.2400-1717T>G		intron	N/A	ENSP00000406012.2	Q96RY7-1
	IFT140	ENST00000361339.9	TSL:1	c.-19-1717T>G		intron	N/A	ENSP00000354895.5	Q96RY7-2
	IFT140	ENST00000889170.1		c.2400-1717T>G		intron	N/A	ENSP00000559229.1

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

African (AFR) AF: 0.0209 AC: 856 AN: 40928

American (AMR) AF: 0.183 AC: 2780 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 395 AN: 3450

East Asian (EAS) AF: 0.142 AC: 722 AN: 5092

South Asian (SAS) AF: 0.0388 AC: 184 AN: 4738

European-Finnish (FIN) AF: 0.0296 AC: 310 AN: 10476

Middle Eastern (MID) AF: 0.0759 AC: 22 AN: 290

European-Non Finnish (NFE) AF: 0.0672 AC: 4545 AN: 67664

Other (OTH) AF: 0.0940 AC: 197 AN: 2096

Alfa AF: 0.00191 Hom.: 0

Bravo AF: 0.0812

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.25
PhyloP100		-1.6
PromoterAI		0.024	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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