11-117869201-A-T

Variant names:

• chr11-117869201-A-T
• rs873713
• NM_022003.4:c.-6+7391T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022003.4(FXYD6):​c.-6+7391T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,254 control chromosomes in the GnomAD database, including 4,105 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 0.20 (4102 hom., cov: 33)
  • Exomes 𝑓: 0.32 (3 hom.)
• Consequence: FXYD6 NM_022003.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 0 publications found

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: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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022003.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FXYD6	NM_022003.4	MANE Select	c.-6+7391T>A		intron	N/A	NP_071286.1	Q9H0Q3-1
	FXYD6-FXYD2	NM_001204268.3		c.-6+7391T>A		intron	N/A	NP_001191197.1	A0A087WZ82
	FXYD6-FXYD2	NM_001243598.4		c.-6+7391T>A		intron	N/A	NP_001230527.1	A0A0A6YYL5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FXYD6	ENST00000526014.6	TSL:1 MANE Select	c.-6+7391T>A		intron	N/A	ENSP00000433312.1	Q9H0Q3-1
	FXYD6-FXYD2	ENST00000614497.5	TSL:3	c.-6+7391T>A		intron	N/A	ENSP00000482442.1	A0A087WZ82
	FXYD6	ENST00000260282.8	TSL:1	c.-179+7391T>A		intron	N/A	ENSP00000260282.4	Q9H0Q3-1

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30789 AN: 152072 Hom.: 4102 Cov.: 33

Gnomad AFR AF: 0.0477

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.212

GnomAD4 exome AF: 0.323 AC: 20 AN: 62 Hom.: 3 Cov.: 0 AF XY: 0.333 AC XY: 12 AN XY: 36

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.455 AC: 10 AN: 22

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.188 AC: 6 AN: 32

Other (OTH) AF: 0.500 AC: 4 AN: 8

GnomAD4 genome AF: 0.202 AC: 30774 AN: 152192 Hom.: 4102 Cov.: 33 AF XY: 0.210 AC XY: 15618 AN XY: 74380

African (AFR) AF: 0.0476 AC: 1977 AN: 41540

American (AMR) AF: 0.329 AC: 5031 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 881 AN: 3472

East Asian (EAS) AF: 0.285 AC: 1473 AN: 5164

South Asian (SAS) AF: 0.296 AC: 1427 AN: 4824

European-Finnish (FIN) AF: 0.342 AC: 3616 AN: 10580

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15536 AN: 68008

Other (OTH) AF: 0.208 AC: 439 AN: 2106

Alfa AF: 0.134 Hom.: 254

Bravo AF: 0.199

Asia WGS AF: 0.263 AC: 913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.71
PhyloP100		-0.22
PromoterAI		0.030	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs873713; hg19: chr11-117739916;