rs11608153

chr11-117845948-A-G

Variant summary

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

The NM_022003.4(FXYD6):c.-5-3167T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,208 control chromosomes in the GnomAD database, including 2,424 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 0.14 (2424 hom., cov: 33)
• Consequence: FXYD6 NM_022003.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119

Genes affected

FXYD6 (HGNC:4030): (FXYD domain containing ion transport regulator 6) This gene encodes a member of the FXYD family of transmembrane proteins. This particular protein encodes phosphohippolin, which likely affects the activity of Na,K-ATPase. Multiple alternatively spliced transcript variants encoding the same protein have been described. Related pseudogenes have been identified on chromosomes 10 and X. Read-through transcripts have been observed between this locus and the downstream sodium/potassium-transporting ATPase subunit gamma (FXYD2, GeneID 486) locus.[provided by RefSeq, Feb 2011]

FXYD6-FXYD2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FXYD6	NM_022003.4	c.-5-3167T>C		intron_variant		ENST00000526014.6
FXYD6-FXYD2	NM_001243598.4	c.-5-3167T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FXYD6	ENST00000526014.6	c.-5-3167T>C		intron_variant		1	NM_022003.4	P1

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21517 AN: 152090 Hom.: 2421 Cov.: 33

Gnomad AFR AF: 0.0285

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.141 AC: 21521 AN: 152208 Hom.: 2424 Cov.: 33 AF XY: 0.154 AC XY: 11464 AN XY: 74418

Gnomad4 AFR AF: 0.0285

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.131

Alfa AF: 0.135 Hom.: 744

Bravo AF: 0.143

Asia WGS AF: 0.248 AC: 859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.57
Dann	Benign	0.48

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: rs11608153; hg19: chr11-117716663;