rs7737031

Variant names:

• chr5-132710898-C-T
• rs7737031
• NM_001300791.2:c.1228+61G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 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=-0.79).
• 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 rank	MANE	Protein	UniProt
KIF3A	NM_001300791.2	c.1228+61G>A		intron_variant	Intron 9 of 18	ENST00000403231.6	NP_001287720.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF3A	ENST00000403231.6	c.1228+61G>A		intron_variant	Intron 9 of 18	2	NM_001300791.2	ENSP00000385808.1

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

African (AFR) AF: 0.388 AC: 12762 AN: 32862

American (AMR) AF: 0.413 AC: 17807 AN: 43138

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 3781 AN: 25728

East Asian (EAS) AF: 0.725 AC: 28668 AN: 39520

South Asian (SAS) AF: 0.154 AC: 13142 AN: 85232

European-Finnish (FIN) AF: 0.341 AC: 18148 AN: 53170

Middle Eastern (MID) AF: 0.120 AC: 688 AN: 5716

European-Non Finnish (NFE) AF: 0.136 AC: 150530 AN: 1106054

Other (OTH) AF: 0.199 AC: 11946 AN: 59938

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

African (AFR) AF: 0.388 AC: 16069 AN: 41410

American (AMR) AF: 0.299 AC: 4563 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 521 AN: 3468

East Asian (EAS) AF: 0.753 AC: 3891 AN: 5166

South Asian (SAS) AF: 0.181 AC: 872 AN: 4824

European-Finnish (FIN) AF: 0.358 AC: 3773 AN: 10548

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10160 AN: 67978

Other (OTH) AF: 0.222 AC: 468 AN: 2112

Alfa AF: 0.220 Hom.: 796

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
PhyloP100		-0.59
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: rs7737031; hg19: chr5-132046590;