Variant chr1-62238632-C-CTT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_181712.5(KANK4):c.2884-253_2884-252dupAA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.24 ( 4443 hom., cov: 0)

Consequence

KANK4
NM_181712.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.48

Variant links:

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]

KANK4 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 1-62238632-C-CTT is Benign according to our data. Variant chr1-62238632-C-CTT is described in ClinVar as [Benign]. Clinvar id is 1241503.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KANK4	NM_181712.5 linkuse as main transcript	c.2884-253_2884-252dupAA		intron_variant		ENST00000371153.9	NP_859063.3	Q5T7N3-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
KANK4	ENST00000371153.9 linkuse as main transcript	c.2884-253_2884-252dupAA	intron_variant	1	NM_181712.5	ENSP00000360195.4	Q5T7N3-1
KANK4	ENST00000354381.3 linkuse as main transcript	c.1000-253_1000-252dupAA	intron_variant	2		ENSP00000346352.3	Q5T7N3-2
KANK4	ENST00000371150.5 linkuse as main transcript	c.952-253_952-252dupAA	intron_variant	2		ENSP00000360192.1	B1ALP6
KANK4	ENST00000317477.8 linkuse as main transcript	c.298-253_298-252dupAA	intron_variant	2		ENSP00000321161.4	B1ALP5

Frequencies

GnomAD3 genomes

AF:

0.235

AC:

33333

AN:

141888

Hom.:

4439

Cov.:

show subpopulations

Gnomad AFR

AF:

0.102

Gnomad AMI

AF:

0.239

Gnomad AMR

AF:

0.259

Gnomad ASJ

AF:

0.256

Gnomad EAS

AF:

0.164

Gnomad SAS

AF:

0.202

Gnomad FIN

AF:

0.323

Gnomad MID

AF:

0.216

Gnomad NFE

AF:

0.305

Gnomad OTH

AF:

0.236

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

GnomAD4 genome

AF:

0.235

AC:

33350

AN:

141904

Hom.:

4443

Cov.:

AF XY:

0.234

AC XY:

16000

AN XY:

68296

show subpopulations

Gnomad4 AFR

AF:

0.102

Gnomad4 AMR

AF:

0.260

Gnomad4 ASJ

AF:

0.256

Gnomad4 EAS

AF:

0.164

Gnomad4 SAS

AF:

0.204

Gnomad4 FIN

AF:

0.323

Gnomad4 NFE

AF:

0.305

Gnomad4 OTH

AF:

0.235

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Oct 25, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over