rs7737031

chr5-132710898-C-T

Variant summary

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

The NM_001300791.2(KIF3A):c.1228+61G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 1,603,332 control chromosomes in the GnomAD database, including 40,539 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 0.27 (7004 hom., cov: 32)
  • Exomes 𝑓: 0.18 (33535 hom.)
• Consequence: KIF3A NM_001300791.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.594

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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF3A	NM_001300791.2	c.1228+61G>A		intron_variant		ENST00000403231.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF3A	ENST00000403231.6	c.1228+61G>A		intron_variant		2	NM_001300791.2
	ENST00000628061.1	n.112-12163C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40331 AN: 151854 Hom.: 7001 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.219

GnomAD4 exome AF: 0.177 AC: 257472 AN: 1451358 Hom.: 33535 AF XY: 0.175 AC XY: 126115 AN XY: 722038

Gnomad4 AFR exome AF: 0.388

Gnomad4 AMR exome AF: 0.413

Gnomad4 ASJ exome AF: 0.147

Gnomad4 EAS exome AF: 0.725

Gnomad4 SAS exome AF: 0.154

Gnomad4 FIN exome AF: 0.341

Gnomad4 NFE exome AF: 0.136

Gnomad4 OTH exome AF: 0.199

GnomAD4 genome AF: 0.266 AC: 40369 AN: 151974 Hom.: 7004 Cov.: 32 AF XY: 0.275 AC XY: 20458 AN XY: 74298

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.222

Alfa AF: 0.214 Hom.: 729

Bravo AF: 0.272

Asia WGS AF: 0.439 AC: 1527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	7.9
Dann	Benign	0.69

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: rs7737031; hg19: chr5-132046590;