rs534494159

Variant names:

• chr2-97196724-T-A
• rs534494159
• NM_001354587.1:c.2589T>A

Your query was ambiguous. Multiple possible variants found:

• chr2-97196724-T-A
• chr2-97196724-T-G

Variant summary

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

The NM_001354587.1(ANKRD36):​c.2589T>A​(p.Ser863Arg) 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. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 48)
• Consequence: ANKRD36 NM_001354587.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138

Genes affected

ANKRD36 (HGNC:24079): (ankyrin repeat domain 36)

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=0.12411907).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD36	NM_001354587.1	c.2589T>A	p.Ser863Arg	missense_variant	Exon 42 of 76	ENST00000420699.9	NP_001341516.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD36	ENST00000420699.9	c.2589T>A	p.Ser863Arg	missense_variant	Exon 42 of 76	5	NM_001354587.1	ENSP00000391950.4
ANKRD36	ENST00000461153.7	c.2589T>A	p.Ser863Arg	missense_variant	Exon 42 of 75	5		ENSP00000419530.3
ANKRD36	ENST00000652721.1	c.2589T>A	p.Ser863Arg	missense_variant	Exon 42 of 76			ENSP00000498611.1

Frequencies

GnomAD3 genomes Cov.: 48

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 48

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.29
BayesDel_addAF	Benign	-0.15	T
BayesDel_noAF	Benign	-0.45
CADD	Benign	9.9
DANN	Uncertain	0.99
DEOGEN2	Benign	0.0051	.;T
Eigen	Benign	-0.55
Eigen_PC	Benign	-0.83
FATHMM_MKL	Benign	0.0068	N
LIST_S2	Benign	0.43	T;T
M_CAP	Benign	0.012	T
MetaRNN	Benign	0.12	T;T
MetaSVM	Benign	-0.58	T
MutationAssessor	Benign	1.4	.;L
PrimateAI	Uncertain	0.68	T
PROVEAN	Benign	0.52	N;N
REVEL	Benign	0.18
Sift	Uncertain	0.0030	D;D
Sift4G	Benign	0.46	T;T
Polyphen		0.94	.;P
Vest4		0.12
MutPred		0.16		Loss of phosphorylation at S863 (P = 0.0096);Loss of phosphorylation at S863 (P = 0.0096);
MVP		0.47
ClinPred		0.22	T
GERP RS		0.67
Varity_R		0.078

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs534494159; hg19: chr2-97862461;