rs885954

Variant names:

• chr9-105647119-A-C
• rs885954
• ENST00000676310.1:c.1271-4953A>C

Your query was ambiguous. Multiple possible variants found:

• chr9-105647119-A-C
• chr9-105647119-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000676310.1(FKTN):​c.1271-4953A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 151,998 control chromosomes in the GnomAD database, including 12,702 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.40 (12702 hom., cov: 32)
• Consequence: FKTN ENST00000676310.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FKTN	ENST00000676310.1	c.1271-4953A>C		intron_variant	Intron 9 of 9			ENSP00000501585.1

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60220 AN: 151880 Hom.: 12678 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.397 AC: 60276 AN: 151998 Hom.: 12702 Cov.: 32 AF XY: 0.394 AC XY: 29269 AN XY: 74294

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.429

Alfa AF: 0.443 Hom.: 22255

Bravo AF: 0.402

Asia WGS AF: 0.274 AC: 952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.4
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs885954; hg19: chr9-108409400;