rs746111216

Variant names:

• chr7-16625039-T-C
• rs746111216
• NM_020319.3:c.314A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-16625039-T-C
• chr7-16625039-T-G

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_020319.3(ANKMY2):​c.314A>G​(p.Glu105Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,810 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E105A) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: ANKMY2 NM_020319.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.61

Genes affected

ANKMY2 (HGNC:25370): (ankyrin repeat and MYND domain containing 2) Predicted to enable enzyme binding activity and metal ion binding activity. Predicted to be located in cilium. [provided by Alliance of Genome Resources, Apr 2022]

LOC105375169 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKMY2	NM_020319.3	c.314A>G	p.Glu105Gly	missense_variant	Exon 4 of 10	ENST00000306999.7	NP_064715.1
LOC105375169	XR_007060226.1	n.420-3241T>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKMY2	ENST00000306999.7	c.314A>G	p.Glu105Gly	missense_variant	Exon 4 of 10	1	NM_020319.3	ENSP00000303570.2
ANKMY2	ENST00000628652.1	c.314A>G	p.Glu105Gly	missense_variant	Exon 4 of 9	5		ENSP00000485738.1
ANKMY2	ENST00000447802.3	n.314A>G		non_coding_transcript_exon_variant	Exon 4 of 11	2		ENSP00000392259.1
ANKMY2	ENST00000453623.5	n.*291A>G		downstream_gene_variant		4		ENSP00000410075.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461810 Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1 AN XY: 727196

African (AFR) AF: 0.00 AC: 0 AN: 33480

American (AMR) AF: 0.00 AC: 0 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26130

East Asian (EAS) AF: 0.00 AC: 0 AN: 39682

South Asian (SAS) AF: 0.00 AC: 0 AN: 86250

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53420

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.00000180 AC: 2 AN: 1111966

Other (OTH) AF: 0.00 AC: 0 AN: 60392

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.22
BayesDel_addAF	Benign	-0.067	T
BayesDel_noAF	Benign	-0.33
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Benign	0.038	T;.
Eigen	Uncertain	0.52
Eigen_PC	Uncertain	0.59
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.94	D;D
M_CAP	Benign	0.030	D
MetaRNN	Uncertain	0.43	T;T
MetaSVM	Benign	-0.89	T
MutationAssessor	Benign	1.1	L;.
PhyloP100		7.6
PrimateAI	Uncertain	0.69	T
PROVEAN	Uncertain	-3.8	D;.
REVEL	Benign	0.23
Sift	Benign	0.094	T;.
Sift4G	Benign	0.20	T;T
Polyphen		0.67	P;.
Vest4		0.40
MutPred		0.52		Gain of catalytic residue at A104 (P = 0.0676);Gain of catalytic residue at A104 (P = 0.0676);
MVP		0.47
MPC		0.21
ClinPred		0.99	D
GERP RS		5.8
Varity_R		0.45
gMVP		0.67
Mutation Taster		=47/53	disease causing

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

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Other links and lift over

dbSNP: rs746111216; hg19: chr7-16664664;