rs10137340

Positions:

• chr14-55584271-T-C

Variant summary

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

The NM_001079521.2(KTN1):​c.-31+3917T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0806 in 152,228 control chromosomes in the GnomAD database, including 537 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 0.081 (537 hom., cov: 32)
• Consequence: KTN1 NM_001079521.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790

Genes affected

KTN1 (HGNC:6467): (kinectin 1) This gene encodes an integral membrane protein that is a member of the kinectin protein family. The encoded protein is primarily localized to the endoplasmic reticulum membrane. This protein binds kinesin and may be involved in intracellular organelle motility. This protein also binds translation elongation factor-delta and may be involved in the assembly of the elongation factor-1 complex. Alternate splicing results in multiple transcript variants of this gene. [provided by RefSeq, Aug 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KTN1	NM_001079521.2	c.-31+3917T>C		intron_variant		ENST00000395314.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KTN1	ENST00000395314.8	c.-31+3917T>C		intron_variant		1	NM_001079521.2	P3

Frequencies

GnomAD3 genomes AF: 0.0806 AC: 12255 AN: 152106 Hom.: 536 Cov.: 32

Gnomad AFR AF: 0.0698

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.0858

Gnomad ASJ AF: 0.0683

Gnomad EAS AF: 0.0142

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0444

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0932

Gnomad OTH AF: 0.0770

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0806 AC: 12275 AN: 152228 Hom.: 537 Cov.: 32 AF XY: 0.0796 AC XY: 5926 AN XY: 74428

Gnomad4 AFR AF: 0.0698

Gnomad4 AMR AF: 0.0857

Gnomad4 ASJ AF: 0.0683

Gnomad4 EAS AF: 0.0141

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0444

Gnomad4 NFE AF: 0.0932

Gnomad4 OTH AF: 0.0814

Alfa AF: 0.0775 Hom.: 101

Bravo AF: 0.0828

Asia WGS AF: 0.0690 AC: 240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.32

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: rs10137340; hg19: chr14-56050989;