rs1547350

chr14-104179989-A-Cchr14-104179989-A-T

Variant summary

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

The NM_015656.2(KIF26A):c.*199A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 507,532 control chromosomes in the GnomAD database, including 74,202 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 0.53 (21839 hom., cov: 31)
  • Exomes 𝑓: 0.54 (52363 hom.)
• Consequence: KIF26A NM_015656.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435

Genes affected

KIF26A (HGNC:20226): (kinesin family member 26A) Predicted to enable microtubule binding activity and microtubule motor activity. Predicted to be involved in enteric nervous system development; negative regulation of signal transduction; and regulation of cell growth by extracellular stimulus. Predicted to be located in cytosol. Predicted to be part of kinesin complex. Predicted to be active in microtubule. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF26A	NM_015656.2	c.*199A>C		3_prime_UTR_variant	15/15	ENST00000423312.7
KIF26A	XM_011536641.3	c.*199A>C		3_prime_UTR_variant	12/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF26A	ENST00000423312.7	c.*199A>C		3_prime_UTR_variant	15/15	5	NM_015656.2	A2
KIF26A	ENST00000315264.7	c.*199A>C		3_prime_UTR_variant	14/14	1		P4
KIF26A	ENST00000697132.1	c.*199A>C		3_prime_UTR_variant	15/15			A2

Frequencies

GnomAD3 genomes AF: 0.534 AC: 80966 AN: 151720 Hom.: 21811 Cov.: 31

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.527

GnomAD4 exome AF: 0.536 AC: 190557 AN: 355694 Hom.: 52363 Cov.: 5 AF XY: 0.534 AC XY: 97911 AN XY: 183230

Gnomad4 AFR exome AF: 0.496

Gnomad4 AMR exome AF: 0.691

Gnomad4 ASJ exome AF: 0.508

Gnomad4 EAS exome AF: 0.649

Gnomad4 SAS exome AF: 0.529

Gnomad4 FIN exome AF: 0.522

Gnomad4 NFE exome AF: 0.521

Gnomad4 OTH exome AF: 0.542

GnomAD4 genome AF: 0.534 AC: 81042 AN: 151838 Hom.: 21839 Cov.: 31 AF XY: 0.537 AC XY: 39815 AN XY: 74202

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.643

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.522

Gnomad4 OTH AF: 0.532

Alfa AF: 0.518 Hom.: 25467

Bravo AF: 0.542

Asia WGS AF: 0.595 AC: 2065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.38
Dann	Benign	0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1547350; hg19: chr14-104646326;