NM_022003.4:c.-6+9867A>G

Variant names:

• chr11-117866725-T-C
• rs876798
• NM_022003.4:c.-6+9867A>G

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+9867A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,170 control chromosomes in the GnomAD database, including 2,311 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 0.17 (2311 hom., cov: 32)
• Consequence: FXYD6 NM_022003.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 5 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FXYD6	NM_022003.4	c.-6+9867A>G		intron_variant	Intron 1 of 7	ENST00000526014.6	NP_071286.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FXYD6	ENST00000526014.6	c.-6+9867A>G		intron_variant	Intron 1 of 7	1	NM_022003.4	ENSP00000433312.1
FXYD6-FXYD2	ENST00000614497.5	c.-6+9867A>G		intron_variant	Intron 1 of 10	3		ENSP00000482442.1

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25381 AN: 152052 Hom.: 2312 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0962

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.167 AC: 25393 AN: 152170 Hom.: 2311 Cov.: 32 AF XY: 0.165 AC XY: 12263 AN XY: 74418

African (AFR) AF: 0.238 AC: 9876 AN: 41474

American (AMR) AF: 0.138 AC: 2105 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 555 AN: 3466

East Asian (EAS) AF: 0.152 AC: 789 AN: 5174

South Asian (SAS) AF: 0.102 AC: 490 AN: 4826

European-Finnish (FIN) AF: 0.0962 AC: 1022 AN: 10622

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9984 AN: 68006

Other (OTH) AF: 0.161 AC: 340 AN: 2116

Alfa AF: 0.153 Hom.: 6961

Bravo AF: 0.173

Asia WGS AF: 0.161 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.0
DANN	Benign	0.68
PhyloP100		1.1
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: rs876798; hg19: chr11-117737440;