Variant 19-11166556-G-A 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.*2C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 1,612,072 control chromosomes in the GnomAD database, including 178,432 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.51 ( 21422 hom., cov: 33)

Exomes 𝑓: 0.46 ( 157010 hom. )

Consequence

KANK2
NM_001136191.3 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.65

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=-0.85).

BP6

Variant 19-11166556-G-A is Benign according to our data. Variant chr19-11166556-G-A is described in ClinVar as [Benign]. Clinvar id is 1295464.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.7 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.*2C>T		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.*2C>T	3_prime_UTR_variant	13/13	1	NM_001136191.3	ENSP00000465650.1	Q63ZY3-1
KANK2	ENST00000588787.5 linkuse as main transcript	c.*2C>T	3_prime_UTR_variant	5/5	5		ENSP00000464896.1	K7EIU4
KANK2	ENST00000587317.1 linkuse as main transcript	n.425C>T	non_coding_transcript_exon_variant	4/4	2
KANK2	ENST00000589359.5 linkuse as main transcript	c.*2C>T	downstream_gene_variant		5		ENSP00000468002.1	Q63ZY3-2

Frequencies

GnomAD3 genomes

AF:

0.514

AC:

78159

AN:

151996

Hom.:

21376

Cov.:

show subpopulations

Gnomad AFR

AF:

0.707

Gnomad AMI

AF:

0.434

Gnomad AMR

AF:

0.373

Gnomad ASJ

AF:

0.502

Gnomad EAS

AF:

0.308

Gnomad SAS

AF:

0.371

Gnomad FIN

AF:

0.452

Gnomad MID

AF:

0.443

Gnomad NFE

AF:

0.467

Gnomad OTH

AF:

0.495

GnomAD3 exomes

AF:

0.435

AC:

108583

AN:

249626

Hom.:

24987

AF XY:

0.436

AC XY:

58834

AN XY:

135072

show subpopulations

Gnomad AFR exome

AF:

0.710

Gnomad AMR exome

AF:

0.300

Gnomad ASJ exome

AF:

0.477

Gnomad EAS exome

AF:

0.312

Gnomad SAS exome

AF:

0.387

Gnomad FIN exome

AF:

0.453

Gnomad NFE exome

AF:

0.462

Gnomad OTH exome

AF:

0.447

GnomAD4 exome

AF:

0.459

AC:

670370

AN:

1459958

Hom.:

157010

Cov.:

AF XY:

0.457

AC XY:

331773

AN XY:

726374

show subpopulations

Gnomad4 AFR exome

AF:

0.717

Gnomad4 AMR exome

AF:

0.305

Gnomad4 ASJ exome

AF:

0.480

Gnomad4 EAS exome

AF:

0.313

Gnomad4 SAS exome

AF:

0.389

Gnomad4 FIN exome

AF:

0.453

Gnomad4 NFE exome

AF:

0.468

Gnomad4 OTH exome

AF:

0.461

GnomAD4 genome

AF:

0.514

AC:

78248

AN:

152114

Hom.:

21422

Cov.:

AF XY:

0.508

AC XY:

37766

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.707

Gnomad4 AMR

AF:

0.373

Gnomad4 ASJ

AF:

0.502

Gnomad4 EAS

AF:

0.309

Gnomad4 SAS

AF:

0.370

Gnomad4 FIN

AF:

0.452

Gnomad4 NFE

AF:

0.467

Gnomad4 OTH

AF:

0.497

Alfa

AF:

0.463

Hom.:

7919

Bravo

AF:

0.518

Asia WGS

AF:

0.376

AC:

1309

AN:

3478

EpiCase

AF:

0.463

EpiControl

AF:

0.469

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	Oct 21, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.021

DANN

Benign

0.89

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