rs1547350

Variant names:

• chr14-104179989-A-C
• rs1547350
• NM_015656.2:c.*199A>C

Your query was ambiguous. Multiple possible variants found:

• chr14-104179989-A-C
• chr14-104179989-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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]

KIF26A Gene-Disease associations (from GenCC):

• complex cortical dysplasia with other brain malformations

  Inheritance: AR Classification: STRONG Submitted by: ClinGen
• cortical dysplasia, complex, with other brain malformations 11

  Inheritance: AR Classification: STRONG, MODERATE, LIMITED Submitted by: Ambry Genetics, Baylor College of Medicine Research Center, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015656.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF26A	NM_015656.2	MANE Select	c.*199A>C		3_prime_UTR	Exon 15 of 15	NP_056471.1	Q9ULI4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF26A	ENST00000423312.7	TSL:5 MANE Select	c.*199A>C		3_prime_UTR	Exon 15 of 15	ENSP00000388241.2	Q9ULI4
	KIF26A	ENST00000315264.7	TSL:1	c.*199A>C		3_prime_UTR	Exon 14 of 14	ENSP00000325452.7	C9JFF0
	KIF26A	ENST00000697132.1		c.*199A>C		3_prime_UTR	Exon 15 of 15	ENSP00000513129.1	A0A8V8TM02

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

African (AFR) AF: 0.496 AC: 4534 AN: 9146

American (AMR) AF: 0.691 AC: 7602 AN: 11004

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 5631 AN: 11092

East Asian (EAS) AF: 0.649 AC: 16076 AN: 24758

South Asian (SAS) AF: 0.529 AC: 10505 AN: 19864

European-Finnish (FIN) AF: 0.522 AC: 12896 AN: 24704

Middle Eastern (MID) AF: 0.501 AC: 822 AN: 1642

European-Non Finnish (NFE) AF: 0.521 AC: 120925 AN: 232156

Other (OTH) AF: 0.542 AC: 11566 AN: 21328

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

African (AFR) AF: 0.504 AC: 20868 AN: 41378

American (AMR) AF: 0.655 AC: 10006 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1766 AN: 3470

East Asian (EAS) AF: 0.643 AC: 3303 AN: 5134

South Asian (SAS) AF: 0.549 AC: 2645 AN: 4820

European-Finnish (FIN) AF: 0.515 AC: 5445 AN: 10570

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.522 AC: 35440 AN: 67890

Other (OTH) AF: 0.532 AC: 1121 AN: 2108

Alfa AF: 0.524 Hom.: 37250

Bravo AF: 0.542

Asia WGS AF: 0.595 AC: 2065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.38
DANN	Benign	0.57
PhyloP100		-0.43
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1547350; hg19: chr14-104646326;