5-14722332-C-T

Variant names:

• chr5-14722332-C-T
• rs27356
• NM_054027.6:c.1012-5497G>A

Variant summary

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

The NM_054027.6(ANKH):​c.1012-5497G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 152,076 control chromosomes in the GnomAD database, including 39,220 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 0.70 (39220 hom., cov: 32)
• Consequence: ANKH NM_054027.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 11 publications found

Genes affected

ANKH (HGNC:15492): (ANKH inorganic pyrophosphate transport regulator) This gene encodes a multipass transmembrane protein that is expressed in joints and other tissues and controls pyrophosphate levels in cultured cells. Progressive ankylosis-mediated control of pyrophosphate levels has been suggested as a possible mechanism regulating tissue calcification and susceptibility to arthritis in higher animals. Mutations in this gene have been associated with autosomal dominant craniometaphyseal dysplasia. [provided by RefSeq, Jul 2008]

ANKH Gene-Disease associations (from GenCC):

• chondrocalcinosis 2

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), G2P
• craniometaphyseal dysplasia, autosomal dominant

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Genomics England PanelApp, G2P, Labcorp Genetics (formerly Invitae)
• skeletal dysplasia

  Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics
• craniometaphyseal dysplasia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_054027.6. 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
	ANKH	NM_054027.6	MANE Select	c.1012-5497G>A		intron	N/A	NP_473368.1	Q9HCJ1-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKH	ENST00000284268.8	TSL:1 MANE Select	c.1012-5497G>A		intron	N/A	ENSP00000284268.6	Q9HCJ1-1
	ANKH	ENST00000887636.1		c.1012-5497G>A		intron	N/A	ENSP00000557695.1
	ANKH	ENST00000964374.1		c.1012-5497G>A		intron	N/A	ENSP00000634433.1

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106393 AN: 151958 Hom.: 39221 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.700 AC: 106418 AN: 152076 Hom.: 39220 Cov.: 32 AF XY: 0.707 AC XY: 52607 AN XY: 74364

African (AFR) AF: 0.439 AC: 18189 AN: 41416

American (AMR) AF: 0.777 AC: 11866 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3081 AN: 3470

East Asian (EAS) AF: 0.779 AC: 4044 AN: 5188

South Asian (SAS) AF: 0.819 AC: 3945 AN: 4816

European-Finnish (FIN) AF: 0.853 AC: 9028 AN: 10588

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53725 AN: 67998

Other (OTH) AF: 0.729 AC: 1542 AN: 2114

Alfa AF: 0.693 Hom.: 7550

Bravo AF: 0.682

Asia WGS AF: 0.747 AC: 2598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.7
DANN	Benign	0.60
PhyloP100		0.024
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: rs27356; hg19: chr5-14722441;