1-62238632-CT-C

Position:

• chr1-62238632-CT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The NM_181712.5(KANK4):​c.2884-252delA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.012 (22 hom., cov: 0)
• Consequence: KANK4 NM_181712.5 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.48

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 1-62238632-CT-C is Benign according to our data. Variant chr1-62238632-CT-C is described in ClinVar as [Likely_benign]. Clinvar id is 1316765.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0119 (1690/142146) while in subpopulation AFR AF= 0.0385 (1496/38906). AF 95% confidence interval is 0.0368. There are 22 homozygotes in gnomad4. There are 789 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 22 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KANK4	NM_181712.5	c.2884-252delA		intron_variant		ENST00000371153.9	NP_859063.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KANK4	ENST00000371153.9	c.2884-252delA		intron_variant		1	NM_181712.5	ENSP00000360195.4
KANK4	ENST00000354381.3	c.1000-252delA		intron_variant		2		ENSP00000346352.3
KANK4	ENST00000371150.5	c.952-252delA		intron_variant		2		ENSP00000360192.1
KANK4	ENST00000317477.8	c.298-252delA		intron_variant		2		ENSP00000321161.4

Frequencies

GnomAD3 genomes AF: 0.0118 AC: 1683 AN: 142128 Hom.: 22 Cov.: 0

Gnomad AFR AF: 0.0384

Gnomad AMI AF: 0.00227

Gnomad AMR AF: 0.00441

Gnomad ASJ AF: 0.000296

Gnomad EAS AF: 0.000820

Gnomad SAS AF: 0.000222

Gnomad FIN AF: 0.00275

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00133

Gnomad OTH AF: 0.00718

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

GnomAD4 genome AF: 0.0119 AC: 1690 AN: 142146 Hom.: 22 Cov.: 0 AF XY: 0.0115 AC XY: 789 AN XY: 68444

Gnomad4 AFR AF: 0.0385

Gnomad4 AMR AF: 0.00447

Gnomad4 ASJ AF: 0.000296

Gnomad4 EAS AF: 0.000822

Gnomad4 SAS AF: 0.000223

Gnomad4 FIN AF: 0.00275

Gnomad4 NFE AF: 0.00133

Gnomad4 OTH AF: 0.00713

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Jan 28, 2020

- -

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: rs199999610; hg19: chr1-62704304;