rs211300

Variant names:

• chr10-32056210-A-G
• rs211300
• NM_004521.3:c.-237T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-32056210-A-G
• chr10-32056210-A-T

Variant summary

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

The NM_004521.3(KIF5B):​c.-237T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 493,216 control chromosomes in the GnomAD database, including 12,325 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 0.21 (3617 hom., cov: 33)
  • Exomes 𝑓: 0.22 (8708 hom.)
• Consequence: KIF5B NM_004521.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.919
• Publications: 5 publications found

Genes affected

KIF5B (HGNC:6324): (kinesin family member 5B) Enables identical protein binding activity; microtubule binding activity; and microtubule motor activity. Involved in several processes, including lysosome localization; natural killer cell mediated cytotoxicity; and positive regulation of protein localization to plasma membrane. Located in centriolar satellite; cytosol; and vesicle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF5B	NM_004521.3	c.-237T>C		5_prime_UTR_variant	Exon 1 of 26	ENST00000302418.5	NP_004512.1
KIF5B	XM_047425202.1	c.-237T>C		5_prime_UTR_variant	Exon 1 of 25		XP_047281158.1
KIF5B	XM_047425203.1	c.-733T>C		5_prime_UTR_variant	Exon 1 of 27		XP_047281159.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF5B	ENST00000302418.5	c.-237T>C		5_prime_UTR_variant	Exon 1 of 26	1	NM_004521.3	ENSP00000307078.4

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32235 AN: 151884 Hom.: 3609 Cov.: 33

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.00796

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.210

GnomAD4 exome AF: 0.219 AC: 74803 AN: 341216 Hom.: 8708 Cov.: 4 AF XY: 0.220 AC XY: 39916 AN XY: 181036

African (AFR) AF: 0.206 AC: 1325 AN: 6420

American (AMR) AF: 0.203 AC: 1778 AN: 8766

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 2344 AN: 10200

East Asian (EAS) AF: 0.00399 AC: 77 AN: 19278

South Asian (SAS) AF: 0.203 AC: 7291 AN: 35914

European-Finnish (FIN) AF: 0.188 AC: 4416 AN: 23506

Middle Eastern (MID) AF: 0.284 AC: 429 AN: 1508

European-Non Finnish (NFE) AF: 0.245 AC: 52910 AN: 215694

Other (OTH) AF: 0.212 AC: 4233 AN: 19930

GnomAD4 genome AF: 0.212 AC: 32280 AN: 152000 Hom.: 3617 Cov.: 33 AF XY: 0.208 AC XY: 15458 AN XY: 74308

African (AFR) AF: 0.203 AC: 8434 AN: 41494

American (AMR) AF: 0.187 AC: 2851 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 814 AN: 3470

East Asian (EAS) AF: 0.00778 AC: 40 AN: 5140

South Asian (SAS) AF: 0.180 AC: 863 AN: 4792

European-Finnish (FIN) AF: 0.183 AC: 1937 AN: 10592

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.245 AC: 16659 AN: 67912

Other (OTH) AF: 0.213 AC: 451 AN: 2114

Alfa AF: 0.116 Hom.: 189

Bravo AF: 0.214

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	11
DANN	Benign	0.85
PhyloP100		0.92
PromoterAI		0.045	Neutral
Mutation Taster		=300/0	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: rs211300; hg19: chr10-32345138;