11-117832217-G-A

Position:

• chr11-117832217-G-A

Variant summary

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

The NM_001204268.3(FXYD6-FXYD2):​c.259+7564C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0205 in 152,302 control chromosomes in the GnomAD database, including 210 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 0.021 (210 hom., cov: 33)
• Consequence: FXYD6-FXYD2 NM_001204268.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231

Genes affected

FXYD6-FXYD2 (HGNC:39978): (FXYD6-FXYD2 readthrough) This locus represents naturally occurring read-through transcription between the neighboring FXYD domain-containing ion transport regulator 6 (GeneID 53826) and sodium/potassium-transporting ATPase subunit gamma (GeneID 486) genes on chromosome 11. One read-through transcript produces a fusion protein that shares sequence identity with each individual gene product, while another read-through transcript encodes a protein that has a distinct C-terminus and only shares sequence identity with the upstream locus (GeneID 53826). [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FXYD6-FXYD2	NM_001204268.3	c.259+7564C>T		intron_variant			NP_001191197.1
FXYD6-FXYD2	NM_001243598.4	c.272+7564C>T		intron_variant			NP_001230527.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FXYD6-FXYD2	ENST00000614497.5	c.259+7564C>T		intron_variant		3		ENSP00000482442.1
FXYD6-FXYD2	ENST00000532984.1	c.272+7564C>T		intron_variant		3		ENSP00000463024.1

Frequencies

GnomAD3 genomes AF: 0.0205 AC: 3124 AN: 152184 Hom.: 211 Cov.: 33

Gnomad AFR AF: 0.00393

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0799

Gnomad ASJ AF: 0.00576

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.00584

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00125

Gnomad OTH AF: 0.0201

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

GnomAD4 genome AF: 0.0205 AC: 3129 AN: 152302 Hom.: 210 Cov.: 33 AF XY: 0.0248 AC XY: 1850 AN XY: 74472

Gnomad4 AFR AF: 0.00392

Gnomad4 AMR AF: 0.0798

Gnomad4 ASJ AF: 0.00576

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.00584

Gnomad4 NFE AF: 0.00125

Gnomad4 OTH AF: 0.0222

Alfa AF: 0.0208 Hom.: 20

Bravo AF: 0.0239

Asia WGS AF: 0.123 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.39
DANN	Benign	0.46

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

Other links and lift over

dbSNP: rs11216573; hg19: chr11-117702932;