1-62247304-CT-C

Position:

• chr1-62247304-CT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_181712.5(KANK4):​c.2883+167delA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0746 in 135,992 control chromosomes in the GnomAD database, including 675 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.075 (675 hom., cov: 28)
• Consequence: KANK4 NM_181712.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.979

Genes affected

KANK4 (HGNC:27263): (KN motif and ankyrin repeat domains 4) Predicted to be involved in negative regulation of actin filament polymerization. Located in cytosol and microtubule cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 1-62247304-CT-C is Benign according to our data. Variant chr1-62247304-CT-C is described in ClinVar as [Benign]. Clinvar id is 1231277.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KANK4	NM_181712.5	c.2883+167delA		intron_variant		ENST00000371153.9	NP_859063.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KANK4	ENST00000371153.9	c.2883+167delA		intron_variant		1	NM_181712.5	ENSP00000360195.4
KANK4	ENST00000354381.3	c.999+167delA		intron_variant		2		ENSP00000346352.3
KANK4	ENST00000371150.5	c.951+167delA		intron_variant		2		ENSP00000360192.1
KANK4	ENST00000317477.8	c.297+167delA		intron_variant		2		ENSP00000321161.4

Frequencies

GnomAD3 genomes AF: 0.0744 AC: 10110 AN: 135956 Hom.: 673 Cov.: 28

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.0142

Gnomad AMR AF: 0.0436

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.0270

Gnomad SAS AF: 0.0214

Gnomad FIN AF: 0.0670

Gnomad MID AF: 0.0294

Gnomad NFE AF: 0.0237

Gnomad OTH AF: 0.0680

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

GnomAD4 genome AF: 0.0746 AC: 10139 AN: 135992 Hom.: 675 Cov.: 28 AF XY: 0.0750 AC XY: 4900 AN XY: 65314

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.0435

Gnomad4 ASJ AF: 0.0314

Gnomad4 EAS AF: 0.0269

Gnomad4 SAS AF: 0.0215

Gnomad4 FIN AF: 0.0670

Gnomad4 NFE AF: 0.0237

Gnomad4 OTH AF: 0.0681

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 20, 2019

- -

Computational scores

Source: dbNSFP v4.3

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: rs371644915; hg19: chr1-62712976;