rs10052744

chr5-14753655-G-A

Variant summary

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

The NM_054027.6(ANKH):c.516+2206C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,030 control chromosomes in the GnomAD database, including 5,706 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 0.24 (5706 hom., cov: 32)
• Consequence: ANKH NM_054027.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKH	NM_054027.6	c.516+2206C>T		intron_variant		ENST00000284268.8
ANKH	XM_011514067.2	c.516+2206C>T		intron_variant
ANKH	XM_017009644.3	c.432+2206C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKH	ENST00000284268.8	c.516+2206C>T		intron_variant		1	NM_054027.6	P1
ANKH	ENST00000503939.5	n.28+2206C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36912 AN: 151912 Hom.: 5700 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0363

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.243 AC: 36949 AN: 152030 Hom.: 5706 Cov.: 32 AF XY: 0.236 AC XY: 17542 AN XY: 74344

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0359

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.230

Alfa AF: 0.233 Hom.: 1111

Bravo AF: 0.254

Asia WGS AF: 0.0540 AC: 192 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.73
Dann	Benign	0.69

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: rs10052744; hg19: chr5-14753764;