rs10901212

chr9-132771634-C-Achr9-132771634-C-Gchr9-132771634-C-T

Variant summary

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

The NM_152572.3(AK8):c.1121+21000G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.825 in 152,110 control chromosomes in the GnomAD database, including 51,840 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 0.82 (51840 hom., cov: 31)
• Consequence: AK8 NM_152572.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228

Genes affected

AK8 (HGNC:26526): (adenylate kinase 8) Enables AMP binding activity and nucleobase-containing compound kinase activity. Involved in nucleoside diphosphate phosphorylation and nucleoside triphosphate biosynthetic process. Located in 9+2 motile cilium. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AK8	NM_152572.3	c.1121+21000G>T		intron_variant		ENST00000298545.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AK8	ENST00000298545.4	c.1121+21000G>T		intron_variant		1	NM_152572.3	P1
AK8	ENST00000476719.1	n.1558+21000G>T		intron_variant, non_coding_transcript_variant		5
AK8	ENST00000477396.5	n.2036+21000G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.825 AC: 125370 AN: 151992 Hom.: 51782 Cov.: 31

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.825 AC: 125484 AN: 152110 Hom.: 51840 Cov.: 31 AF XY: 0.827 AC XY: 61516 AN XY: 74380

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.862

Gnomad4 ASJ AF: 0.838

Gnomad4 EAS AF: 0.882

Gnomad4 SAS AF: 0.880

Gnomad4 FIN AF: 0.840

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.822

Alfa AF: 0.826 Hom.: 88005

Bravo AF: 0.825

Asia WGS AF: 0.892 AC: 3103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.77
Dann	Benign	0.44

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: rs10901212; hg19: chr9-135647021;