5-14794759-C-T

Position:

• chr5-14794759-C-T

Variant summary

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

The NM_054027.6(ANKH):​c.97-25568G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 152,132 control chromosomes in the GnomAD database, including 31,023 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 0.63 (31023 hom., cov: 33)
• Consequence: ANKH NM_054027.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKH	NM_054027.6	c.97-25568G>A		intron_variant		ENST00000284268.8
ANKH	XM_011514067.2	c.97-25568G>A		intron_variant
ANKH	XM_017009644.3	c.12+1459G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKH	ENST00000284268.8	c.97-25568G>A		intron_variant		1	NM_054027.6	P1
ANKH	ENST00000513115.1	n.122-25568G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96294 AN: 152014 Hom.: 30957 Cov.: 33

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.838

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.634 AC: 96426 AN: 152132 Hom.: 31023 Cov.: 33 AF XY: 0.639 AC XY: 47538 AN XY: 74364

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.837

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.584

Alfa AF: 0.566 Hom.: 40854

Bravo AF: 0.637

Asia WGS AF: 0.783 AC: 2721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.40
DANN	Benign	0.28

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: rs879253; hg19: chr5-14794868;