10-32056210-A-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_004521.3(KIF5B):​c.-237T>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000142 in 493,814 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000013 (0 hom., cov: 33)
  • Exomes 𝑓: 0.000015 (0 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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BS2: High AC in GnomAdExome4 at 5 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF5B	NM_004521.3	c.-237T>A		5_prime_UTR_variant	Exon 1 of 26	ENST00000302418.5	NP_004512.1
KIF5B	XM_047425202.1	c.-237T>A		5_prime_UTR_variant	Exon 1 of 25		XP_047281158.1
KIF5B	XM_047425203.1	c.-733T>A		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>A		5_prime_UTR_variant	Exon 1 of 26	1	NM_004521.3	ENSP00000307078.4

Frequencies

GnomAD3 genomes AF: 0.0000132 AC: 2 AN: 151916 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000146 AC: 5 AN: 341898 Hom.: 0 Cov.: 4 AF XY: 0.0000110 AC XY: 2 AN XY: 181378

African (AFR) AF: 0.00 AC: 0 AN: 6432

American (AMR) AF: 0.00 AC: 0 AN: 8796

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10220

East Asian (EAS) AF: 0.00 AC: 0 AN: 19280

South Asian (SAS) AF: 0.00 AC: 0 AN: 35966

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 23558

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1514

European-Non Finnish (NFE) AF: 0.0000185 AC: 4 AN: 216148

Other (OTH) AF: 0.0000500 AC: 1 AN: 19984

GnomAD4 genome AF: 0.0000132 AC: 2 AN: 151916 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 74198

African (AFR) AF: 0.00 AC: 0 AN: 41382

American (AMR) AF: 0.00 AC: 0 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5152

South Asian (SAS) AF: 0.00 AC: 0 AN: 4796

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10594

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 314

European-Non Finnish (NFE) AF: 0.0000294 AC: 2 AN: 67936

Other (OTH) AF: 0.00 AC: 0 AN: 2092

Alfa AF: 0.00 Hom.: 189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	10
DANN	Benign	0.92
PhyloP100		0.92
PromoterAI		0.041	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.3

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;