rs17691077

Variant names:

• chr5-132707659-A-C
• rs17691077
• NM_001300791.2:c.1301-1200T>G

Your query was ambiguous. Multiple possible variants found:

• chr5-132707659-A-C
• chr5-132707659-A-G
• chr5-132707659-A-T

Variant summary

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

The NM_001300791.2(KIF3A):​c.1301-1200T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0815 in 152,210 control chromosomes in the GnomAD database, including 655 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 0.082 (655 hom., cov: 32)
• Consequence: KIF3A NM_001300791.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158
• Publications: 13 publications found

Genes affected

KIF3A (HGNC:6319): (kinesin family member 3A) Enables protein phosphatase binding activity; small GTPase binding activity; and spectrin binding activity. Involved in protein localization to cell junction and protein transport. Located in centriole and centrosome. Part of kinesin II complex. Colocalizes with spindle microtubule. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000230612 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001300791.2. 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
	KIF3A	NM_001300791.2	MANE Select	c.1301-1200T>G		intron	N/A	NP_001287720.1	E9PES4
	KIF3A	NM_001300792.2		c.1229-1200T>G		intron	N/A	NP_001287721.1	J3KPF9
	KIF3A	NM_007054.7		c.1228+3300T>G		intron	N/A	NP_008985.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF3A	ENST00000403231.6	TSL:2 MANE Select	c.1301-1200T>G		intron	N/A	ENSP00000385808.1	E9PES4
	KIF3A	ENST00000378735.5	TSL:1	c.1229-1200T>G		intron	N/A	ENSP00000368009.1	J3KPF9
	KIF3A	ENST00000618515.4	TSL:5	c.1298-1200T>G		intron	N/A	ENSP00000483023.1	A0A087X011

Frequencies

GnomAD3 genomes AF: 0.0816 AC: 12413 AN: 152092 Hom.: 655 Cov.: 32

Gnomad AFR AF: 0.0229

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.0984

Gnomad ASJ AF: 0.0956

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0513

Gnomad FIN AF: 0.0759

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.0980

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

GnomAD4 genome AF: 0.0815 AC: 12408 AN: 152210 Hom.: 655 Cov.: 32 AF XY: 0.0787 AC XY: 5860 AN XY: 74416

African (AFR) AF: 0.0228 AC: 947 AN: 41526

American (AMR) AF: 0.0983 AC: 1502 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0956 AC: 331 AN: 3464

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.0512 AC: 247 AN: 4826

European-Finnish (FIN) AF: 0.0759 AC: 805 AN: 10604

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8184 AN: 68002

Other (OTH) AF: 0.0965 AC: 204 AN: 2114

Alfa AF: 0.0932 Hom.: 1256

Bravo AF: 0.0809

Asia WGS AF: 0.0210 AC: 71 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.42
PhyloP100		0.16
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: rs17691077; hg19: chr5-132043351;