Variant rs118064041 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_001079802.2(FKTN):c.1044+44A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0323 in 1,509,854 control chromosomes in the GnomAD database, including 904 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.024 ( 58 hom., cov: 32)

Exomes 𝑓: 0.033 ( 846 hom. )

Consequence

FKTN
NM_001079802.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.363

Variant links:

Genes affected

FKTN (HGNC:3622): (fukutin) The protein encoded by this gene is a putative transmembrane protein that is localized to the cis-Golgi compartment, where it may be involved in the glycosylation of alpha-dystroglycan in skeletal muscle. The encoded protein is thought to be a glycosyltransferase and could play a role in brain development. Defects in this gene are a cause of Fukuyama-type congenital muscular dystrophy (FCMD), Walker-Warburg syndrome (WWS), limb-girdle muscular dystrophy type 2M (LGMD2M), and dilated cardiomyopathy type 1X (CMD1X). Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Nov 2010]

FKTN links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP6

Variant 9-105618136-A-G is Benign according to our data. Variant chr9-105618136-A-G is described in ClinVar as [Benign]. Clinvar id is 260021.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-105618136-A-G is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0243 (3699/152192) while in subpopulation NFE AF= 0.0385 (2619/67998). AF 95% confidence interval is 0.0373. There are 58 homozygotes in gnomad4. There are 1689 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 58 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FKTN	NM_001079802.2 linkuse as main transcript	c.1044+44A>G		intron_variant		ENST00000357998.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FKTN	ENST00000357998.10 linkuse as main transcript	c.1044+44A>G		intron_variant		5	NM_001079802.2	P1	O75072-1

Frequencies

GnomAD3 genomes

AF:

0.0243

AC:

3698

AN:

152074

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00688

Gnomad AMI

AF:

0.0198

Gnomad AMR

AF:

0.0173

Gnomad ASJ

AF:

0.0337

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00747

Gnomad FIN

AF:

0.0281

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0385

Gnomad OTH

AF:

0.0279

GnomAD3 exomes

AF:

0.0267

AC:

6635

AN:

248588

Hom.:

119

AF XY:

0.0271

AC XY:

3663

AN XY:

134978

show subpopulations

Gnomad AFR exome

AF:

0.00672

Gnomad AMR exome

AF:

0.0152

Gnomad ASJ exome

AF:

0.0297

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00925

Gnomad FIN exome

AF:

0.0314

Gnomad NFE exome

AF:

0.0409

Gnomad OTH exome

AF:

0.0258

GnomAD4 exome

AF:

0.0332

AC:

45085

AN:

1357662

Hom.:

846

Cov.:

AF XY:

0.0327

AC XY:

22292

AN XY:

681274

show subpopulations

Gnomad4 AFR exome

AF:

0.00536

Gnomad4 AMR exome

AF:

0.0161

Gnomad4 ASJ exome

AF:

0.0283

Gnomad4 EAS exome

AF:

0.0000515

Gnomad4 SAS exome

AF:

0.00952

Gnomad4 FIN exome

AF:

0.0316

Gnomad4 NFE exome

AF:

0.0387

Gnomad4 OTH exome

AF:

0.0277

GnomAD4 genome

AF:

0.0243

AC:

3699

AN:

152192

Hom.:

Cov.:

AF XY:

0.0227

AC XY:

1689

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.00686

Gnomad4 AMR

AF:

0.0173

Gnomad4 ASJ

AF:

0.0337

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00768

Gnomad4 FIN

AF:

0.0281

Gnomad4 NFE

AF:

0.0385

Gnomad4 OTH

AF:

0.0276

Alfa

AF:

0.0334

Hom.:

Bravo

AF:

0.0241

Asia WGS

AF:

0.00433

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

8.4

DANN

Benign

0.73

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