Variant 19-11166398-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001136191.3(KANK2):c.*160G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 655,720 control chromosomes in the GnomAD database, including 55,979 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.37 ( 10892 hom., cov: 32)

Exomes 𝑓: 0.42 ( 45087 hom. )

Consequence

KANK2
NM_001136191.3 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.645

Variant links:

Genes affected

KANK2 (HGNC:29300): (KN motif and ankyrin repeat domains 2) This gene encodes a member of the KN motif and ankyrin repeat domains (KANK) family of proteins, which play a role in cytoskeletal formation by regulating actin polymerization. The encoded protein functions in the sequestration of steroid receptor coactivators and possibly other proteins. Mutations in this gene are associated with impaired kidney podocyte function and nephrotic syndrome, and keratoderma and woolly hair. [provided by RefSeq, Jul 2016]

KANK2 links:

KANK2 (HGNC:):

KANK2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 19-11166398-C-T is Benign according to our data. Variant chr19-11166398-C-T is described in ClinVar as [Benign]. Clinvar id is 1245036.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KANK2	NM_001136191.3 linkuse as main transcript	c.*160G>A		3_prime_UTR_variant	13/13	ENST00000586659.6	NP_001129663.1	Q63ZY3-1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
KANK2	ENST00000586659.6 linkuse as main transcript	c.*160G>A	3_prime_UTR_variant	13/13	1	NM_001136191.3	ENSP00000465650.1	Q63ZY3-1
KANK2	ENST00000588787.5 linkuse as main transcript	c.*160G>A	3_prime_UTR_variant	5/5	5		ENSP00000464896.1	K7EIU4
KANK2	ENST00000587317.1 linkuse as main transcript	n.583G>A	non_coding_transcript_exon_variant	4/4	2

Frequencies

GnomAD3 genomes

AF:

0.372

AC:

56451

AN:

151954

Hom.:

10888

Cov.:

show subpopulations

Gnomad AFR

AF:

0.261

Gnomad AMI

AF:

0.476

Gnomad AMR

AF:

0.454

Gnomad ASJ

AF:

0.423

Gnomad EAS

AF:

0.472

Gnomad SAS

AF:

0.529

Gnomad FIN

AF:

0.349

Gnomad MID

AF:

0.424

Gnomad NFE

AF:

0.400

Gnomad OTH

AF:

0.396

GnomAD4 exome

AF:

0.420

AC:

211544

AN:

503648

Hom.:

45087

Cov.:

AF XY:

0.427

AC XY:

112917

AN XY:

264470

show subpopulations

Gnomad4 AFR exome

AF:

0.272

Gnomad4 AMR exome

AF:

0.471

Gnomad4 ASJ exome

AF:

0.430

Gnomad4 EAS exome

AF:

0.438

Gnomad4 SAS exome

AF:

0.520

Gnomad4 FIN exome

AF:

0.351

Gnomad4 NFE exome

AF:

0.413

Gnomad4 OTH exome

AF:

0.412

GnomAD4 genome

AF:

0.371

AC:

56477

AN:

152072

Hom.:

10892

Cov.:

AF XY:

0.373

AC XY:

27742

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.261

Gnomad4 AMR

AF:

0.454

Gnomad4 ASJ

AF:

0.423

Gnomad4 EAS

AF:

0.473

Gnomad4 SAS

AF:

0.529

Gnomad4 FIN

AF:

0.349

Gnomad4 NFE

AF:

0.400

Gnomad4 OTH

AF:

0.395

Alfa

AF:

0.309

Hom.:

1351

Bravo

AF:

0.371

Asia WGS

AF:

0.454

AC:

1579

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

1.6

DANN

Benign

0.88

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

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