rs137853203

Variant names:

• chr9-127868346-T-A
• NM_000476.3:c.491A>T

Your query was ambiguous. Multiple possible variants found:

• chr9-127868346-T-A
• chr9-127868346-T-C

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2 PP3_Strong

The NM_000476.3(AK1):​c.491A>T​(p.Tyr164Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000275 in 1,452,070 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000028 (0 hom.)
• Consequence: AK1 NM_000476.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.57

Genes affected

AK1 (HGNC:361): (adenylate kinase 1) This gene encodes an adenylate kinase enzyme involved in energy metabolism and homeostasis of cellular adenine nucleotide ratios in different intracellular compartments. This gene is highly expressed in skeletal muscle, brain and erythrocytes. Certain mutations in this gene resulting in a functionally inadequate enzyme are associated with a rare genetic disorder causing nonspherocytic hemolytic anemia. Alternative splicing of this gene results in multiple transcript variants encoding different isoforms. This gene shares readthrough transcripts with the upstream ST6GALNAC6 gene. [provided by RefSeq, Jan 2022]

ENSG00000257524 (HGNC:):

ACMG classification

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.979

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AK1	NM_000476.3	c.491A>T	p.Tyr164Phe	missense_variant	Exon 6 of 7	ENST00000644144.2	NP_000467.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AK1	ENST00000644144.2	c.491A>T	p.Tyr164Phe	missense_variant	Exon 6 of 7		NM_000476.3	ENSP00000494600.1
ENSG00000257524	ENST00000646171.1	n.*524A>T		non_coding_transcript_exon_variant	Exon 12 of 13			ENSP00000495484.1
ENSG00000257524	ENST00000646171.1	n.*524A>T		3_prime_UTR_variant	Exon 12 of 13			ENSP00000495484.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000275 AC: 4 AN: 1452070 Hom.: 0 Cov.: 32 AF XY: 0.00000277 AC XY: 2 AN XY: 721320

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000361

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.27
BayesDel_addAF	Pathogenic	0.21	D
BayesDel_noAF	Uncertain	0.060
CADD	Uncertain	25
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.75	D;D;D;.
Eigen	Uncertain	0.68
Eigen_PC	Uncertain	0.65
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Pathogenic	0.98	.;.;D;D
M_CAP	Uncertain	0.089	D
MetaRNN	Pathogenic	0.98	D;D;D;D
MetaSVM	Uncertain	0.39	D
MutationAssessor	Uncertain	2.2	M;M;M;.
PrimateAI	Uncertain	0.68	T
PROVEAN	Uncertain	-3.6	D;.;D;D
REVEL	Pathogenic	0.78
Sift	Benign	0.038	D;.;D;D
Sift4G	Benign	0.092	T;.;T;D
Polyphen		0.98	D;D;D;.
Vest4		0.54
MutPred		0.94		Loss of MoRF binding (P = 0.1151);Loss of MoRF binding (P = 0.1151);Loss of MoRF binding (P = 0.1151);.;
MVP		0.74
MPC		0.91
ClinPred		0.98	D
GERP RS		5.3
Varity_R		0.80
gMVP		0.87

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr9-130630625;