rs10901212

Variant names:

• chr9-132771634-C-A
• rs10901212
• NM_152572.3:c.1121+21000G>T

Your query was ambiguous. Multiple possible variants found:

• chr9-132771634-C-A
• chr9-132771634-C-G
• chr9-132771634-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
AK8	NM_152572.3	c.1121+21000G>T		intron_variant	Intron 11 of 12	ENST00000298545.4	NP_689785.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AK8	ENST00000298545.4	c.1121+21000G>T		intron_variant	Intron 11 of 12	1	NM_152572.3	ENSP00000298545.3
AK8	ENST00000476719.1	n.1558+21000G>T		intron_variant	Intron 10 of 11	5
AK8	ENST00000477396.5	n.2036+21000G>T		intron_variant	Intron 13 of 14	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

African (AFR) AF: 0.798 AC: 33093 AN: 41474

American (AMR) AF: 0.862 AC: 13178 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.838 AC: 2909 AN: 3472

East Asian (EAS) AF: 0.882 AC: 4556 AN: 5164

South Asian (SAS) AF: 0.880 AC: 4236 AN: 4816

European-Finnish (FIN) AF: 0.840 AC: 8904 AN: 10596

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55976 AN: 67984

Other (OTH) AF: 0.822 AC: 1740 AN: 2116

Alfa AF: 0.826 Hom.: 211272

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
PhyloP100		-0.23
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: rs10901212; hg19: chr9-135647021;