5-138180092-G-C

Position:

• chr5-138180092-G-C

Variant summary

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

The ENST00000394894.8(KIF20A):​c.165+247G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 152,120 control chromosomes in the GnomAD database, including 39,895 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 0.72 (39895 hom., cov: 32)
• Consequence: KIF20A ENST00000394894.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59

Genes affected

KIF20A (HGNC:9787): (kinesin family member 20A) Enables protein kinase binding activity. Involved in microtubule bundle formation; midbody abscission; and regulation of cytokinesis. Located in several cellular components, including cleavage furrow; intercellular bridge; and midbody. Implicated in restrictive cardiomyopathy. [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=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF20A	NM_005733.3	c.165+247G>C		intron_variant		ENST00000394894.8	NP_005724.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF20A	ENST00000394894.8	c.165+247G>C		intron_variant		1	NM_005733.3	ENSP00000378356	P1

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109419 AN: 152002 Hom.: 39840 Cov.: 32

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.720 AC: 109528 AN: 152120 Hom.: 39895 Cov.: 32 AF XY: 0.715 AC XY: 53122 AN XY: 74332

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.716

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.789

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.763

Gnomad4 OTH AF: 0.714

Alfa AF: 0.729 Hom.: 4798

Bravo AF: 0.716

Asia WGS AF: 0.628 AC: 2183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.1
DANN	Benign	0.84

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: rs10038448; hg19: chr5-137515781;