chr14-55584271-T-C

Variant names:

• chr14-55584271-T-C
• rs10137340
• NM_001079521.2:c.-31+3917T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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]

ENSG00000296983 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
KTN1	NM_001079521.2	c.-31+3917T>C		intron_variant	Intron 1 of 43	ENST00000395314.8	NP_001072989.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KTN1	ENST00000395314.8	c.-31+3917T>C		intron_variant	Intron 1 of 43	1	NM_001079521.2	ENSP00000378725.3

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

African (AFR) AF: 0.0698 AC: 2899 AN: 41530

American (AMR) AF: 0.0857 AC: 1310 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0683 AC: 237 AN: 3468

East Asian (EAS) AF: 0.0141 AC: 73 AN: 5186

South Asian (SAS) AF: 0.116 AC: 558 AN: 4828

European-Finnish (FIN) AF: 0.0444 AC: 471 AN: 10614

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0932 AC: 6335 AN: 68000

Other (OTH) AF: 0.0814 AC: 172 AN: 2114

Alfa AF: 0.0769 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
PhyloP100		-0.079
Mutation Taster		=100/0	polymorphism (auto)

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: rs10137340; hg19: chr14-56050989;