rs2491015

chr10-69007057-C-T

Variant summary

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

The NM_015634.4(KIFBP):c.789+1142C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 151,986 control chromosomes in the GnomAD database, including 6,523 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 0.26 (6523 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: KIFBP NM_015634.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.368

Genes affected

KIFBP (HGNC:23419): (kinesin family binding protein) This gene encodes a kinesin family member 1 binding protein that is characterized by two tetratrico peptide repeats. The encoded protein localizes to the mitochondria and may be involved in regulating transport of the mitochondria. Mutations in this gene are associated with Goldberg-Shprintzen megacolon syndrome. [provided by RefSeq, Mar 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIFBP	NM_015634.4	c.789+1142C>T		intron_variant		ENST00000361983.7
KIFBP	XM_017016067.2	c.-704C>T		5_prime_UTR_variant	1/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIFBP	ENST00000361983.7	c.789+1142C>T		intron_variant		1	NM_015634.4	P1

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39835 AN: 151868 Hom.: 6527 Cov.: 32

Gnomad AFR AF: 0.0670

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.299

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.262 AC: 39814 AN: 151986 Hom.: 6523 Cov.: 32 AF XY: 0.259 AC XY: 19213 AN XY: 74308

Gnomad4 AFR AF: 0.0668

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.298

Alfa AF: 0.334 Hom.: 4317

Bravo AF: 0.253

Asia WGS AF: 0.264 AC: 917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
Cadd	Benign	11
Dann	Benign	0.68

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

Publications

LitVar

Other links and lift over

dbSNP: rs2491015; hg19: chr10-70766813;