rs648576

chr1-169930286-C-T

Variant summary

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

The NM_014970.4(KIFAP3):c.2274-8505G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 151,990 control chromosomes in the GnomAD database, including 4,658 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 0.24 (4658 hom., cov: 32)
• Consequence: KIFAP3 NM_014970.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720

Genes affected

KIFAP3 (HGNC:17060): (kinesin associated protein 3) The small G protein GDP dissociation stimulator (smg GDS) is a regulator protein having two activities on a group of small G proteins including the Rho and Rap1 family members and Ki-Ras; one is to stimulate their GDP/GTP exchange reactions, and the other is to inhibit their interactions with membranes. The protein encoded by this gene contains 9 'Armadillo' repeats and interacts with the smg GDS protein through these repeats. This protein, which is highly concentrated around the endoplasmic reticulum, is phosphorylated by v-src, and this phosphorylation reduces the affinity of the protein for smg GDS. It is thought that this protein serves as a linker between human chromosome-associated polypeptide (HCAP) and KIF3A/B, a kinesin superfamily protein in the nucleus, and that it plays a role in the interaction of chromosomes with an ATPase motor protein. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIFAP3	NM_014970.4	c.2274-8505G>A		intron_variant		ENST00000361580.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIFAP3	ENST00000361580.7	c.2274-8505G>A		intron_variant		1	NM_014970.4	P1
KIFAP3	ENST00000367767.5	c.2142-8505G>A		intron_variant		1
KIFAP3	ENST00000367765.5	c.2154-8505G>A		intron_variant		2
KIFAP3	ENST00000538366.5	c.2040-8505G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36037 AN: 151872 Hom.: 4657 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.00597

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.237 AC: 36032 AN: 151990 Hom.: 4658 Cov.: 32 AF XY: 0.233 AC XY: 17339 AN XY: 74266

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.00618

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.239

Alfa AF: 0.277 Hom.: 8284

Bravo AF: 0.229

Asia WGS AF: 0.0690 AC: 241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.8
Dann	Benign	0.67

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: rs648576; hg19: chr1-169899427;