chr11-117831975-C-T

Variant names:

• chr11-117831975-C-T
• rs10790212
• ENST00000614497.5:c.259+7806G>A

Variant summary

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

The ENST00000614497.5(FXYD6-FXYD2):​c.259+7806G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 152,152 control chromosomes in the GnomAD database, including 9,514 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 0.33 (9514 hom., cov: 33)
• Consequence: FXYD6-FXYD2 ENST00000614497.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157
• Publications: 11 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FXYD6-FXYD2	NM_001204268.3	c.259+7806G>A		intron_variant	Intron 6 of 10		NP_001191197.1
FXYD6-FXYD2	NM_001243598.4	c.272+7806G>A		intron_variant	Intron 6 of 9		NP_001230527.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FXYD6-FXYD2	ENST00000614497.5	c.259+7806G>A		intron_variant	Intron 6 of 10	3		ENSP00000482442.1
FXYD6-FXYD2	ENST00000532984.1	c.272+7806G>A		intron_variant	Intron 6 of 9	3		ENSP00000463024.1

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50148 AN: 152034 Hom.: 9489 Cov.: 33

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.330 AC: 50220 AN: 152152 Hom.: 9514 Cov.: 33 AF XY: 0.322 AC XY: 23983 AN XY: 74402

African (AFR) AF: 0.522 AC: 21638 AN: 41470

American (AMR) AF: 0.335 AC: 5121 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1052 AN: 3470

East Asian (EAS) AF: 0.156 AC: 808 AN: 5190

South Asian (SAS) AF: 0.232 AC: 1121 AN: 4826

European-Finnish (FIN) AF: 0.195 AC: 2067 AN: 10598

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17489 AN: 67980

Other (OTH) AF: 0.302 AC: 639 AN: 2116

Alfa AF: 0.289 Hom.: 11444

Bravo AF: 0.353

Asia WGS AF: 0.227 AC: 791 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	3.4
DANN	Benign	0.74
PhyloP100		0.16
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: rs10790212; hg19: chr11-117702690;