5-132700797-A-T

Position:

• chr5-132700797-A-T

Variant summary

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

The NM_001300791.2(KIF3A):​c.1885-97T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 727,418 control chromosomes in the GnomAD database, including 161,863 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 0.59 (28776 hom., cov: 33)
  • Exomes 𝑓: 0.66 (133087 hom.)
• Consequence: KIF3A NM_001300791.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF3A	NM_001300791.2	c.1885-97T>A		intron_variant		ENST00000403231.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF3A	ENST00000403231.6	c.1885-97T>A		intron_variant		2	NM_001300791.2
	ENST00000628061.1	n.111+10963A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90066 AN: 151968 Hom.: 28777 Cov.: 33

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.636

GnomAD4 exome AF: 0.662 AC: 380919 AN: 575332 Hom.: 133087 AF XY: 0.667 AC XY: 205399 AN XY: 308160

Gnomad4 AFR exome AF: 0.414

Gnomad4 AMR exome AF: 0.466

Gnomad4 ASJ exome AF: 0.721

Gnomad4 EAS exome AF: 0.192

Gnomad4 SAS exome AF: 0.665

Gnomad4 FIN exome AF: 0.551

Gnomad4 NFE exome AF: 0.740

Gnomad4 OTH exome AF: 0.660

GnomAD4 genome AF: 0.592 AC: 90091 AN: 152086 Hom.: 28776 Cov.: 33 AF XY: 0.581 AC XY: 43167 AN XY: 74332

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.647

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.634

Alfa AF: 0.529 Hom.: 1584

Bravo AF: 0.580

Asia WGS AF: 0.448 AC: 1553 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.9
DANN	Benign	0.75

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: rs1468215; hg19: chr5-132036489; COSMIC: COSV66413638; COSMIC: COSV66413638;