1-170002351-T-C

Variant names:

• chr1-170002351-T-C
• rs4656729
• NM_014970.4:c.1184-10096A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014970.4(KIFAP3):​c.1184-10096A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,954 control chromosomes in the GnomAD database, including 17,746 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 0.48 (17746 hom., cov: 32)
• Consequence: KIFAP3 NM_014970.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIFAP3	NM_014970.4	c.1184-10096A>G		intron_variant	Intron 10 of 19	ENST00000361580.7	NP_055785.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIFAP3	ENST00000361580.7	c.1184-10096A>G		intron_variant	Intron 10 of 19	1	NM_014970.4	ENSP00000354560.2

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72313 AN: 151836 Hom.: 17711 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.476 AC: 72400 AN: 151954 Hom.: 17746 Cov.: 32 AF XY: 0.483 AC XY: 35834 AN XY: 74258

African (AFR) AF: 0.501 AC: 20775 AN: 41446

American (AMR) AF: 0.504 AC: 7698 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1313 AN: 3464

East Asian (EAS) AF: 0.835 AC: 4328 AN: 5182

South Asian (SAS) AF: 0.510 AC: 2460 AN: 4822

European-Finnish (FIN) AF: 0.499 AC: 5270 AN: 10562

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 29020 AN: 67908

Other (OTH) AF: 0.488 AC: 1028 AN: 2106

Alfa AF: 0.442 Hom.: 28012

Bravo AF: 0.483

Asia WGS AF: 0.652 AC: 2266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.5
DANN	Benign	0.71
PhyloP100		0.34
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: rs4656729; hg19: chr1-169971492;