rs557142117

Variant names:

• chr13-19993212-A-C
• rs557142117
• NM_197968.4:c.140A>C

Your query was ambiguous. Multiple possible variants found:

• chr13-19993212-A-C
• chr13-19993212-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_197968.4(ZMYM2):​c.140A>C​(p.Asn47Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. 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. N47S) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZMYM2 NM_197968.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.107

Genes affected

ZMYM2 (HGNC:12989): (zinc finger MYM-type containing 2) The protein encoded by this gene is a zinc finger protein that may act as a transcription factor. The encoded protein may be part of a BHC histone deacetylase complex. Translocation of this gene with the fibroblast growth factor receptor-1 gene (FGFR1) results in a fusion gene, which may be a cause of stem cell leukemia lymphoma syndrome (SCLL). Several transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2010]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.09208846).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZMYM2	NM_197968.4	c.140A>C	p.Asn47Thr	missense_variant	Exon 3 of 25	ENST00000610343.5	NP_932072.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZMYM2	ENST00000610343.5	c.140A>C	p.Asn47Thr	missense_variant	Exon 3 of 25	1	NM_197968.4	ENSP00000479904.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.076
BayesDel_addAF	Benign	-0.30	T
BayesDel_noAF	Benign	-0.67
CADD	Benign	15
DANN	Benign	0.97
DEOGEN2	Benign	0.24	T;T;T;T
Eigen	Benign	-0.69
Eigen_PC	Benign	-0.63
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Benign	0.68	T;.;.;T
M_CAP	Benign	0.0055	T
MetaRNN	Benign	0.092	T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.69	N;N;N;.
PrimateAI	Benign	0.26	T
PROVEAN	Benign	-1.6	.;N;N;.
REVEL	Benign	0.046
Sift	Benign	0.046	.;D;D;.
Sift4G	Benign	0.090	T;T;T;T
Polyphen		0.0050	B;B;B;.
Vest4		0.21
MutPred		0.28		Gain of catalytic residue at L42 (P = 0.0057);Gain of catalytic residue at L42 (P = 0.0057);Gain of catalytic residue at L42 (P = 0.0057);Gain of catalytic residue at L42 (P = 0.0057);
MVP		0.25
ClinPred		0.12	T
GERP RS		-4.6
Varity_R		0.099
gMVP		0.081

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: rs557142117; hg19: chr13-20567352;