13-110893214-C-T

Variant names:

• chr13-110893214-C-T
• rs2065130543
• NM_017664.4:c.505G>A

Variant summary

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

The NM_017664.4(ANKRD10):​c.505G>A​(p.Gly169Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ANKRD10 NM_017664.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 7.18
• Publications: 0 publications found

Genes affected

ANKRD10 (HGNC:20265): (ankyrin repeat domain 10)

ACMG classification

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

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017664.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD10	NM_017664.4	MANE Select	c.505G>A	p.Gly169Ser	missense	Exon 4 of 6	NP_060134.2	Q9NXR5-1
	ANKRD10	NM_001286721.3		c.599G>A	p.Gly200Glu	missense	Exon 5 of 5	NP_001273650.1	Q9NXR5-2
	ANKRD10	NR_104586.3		n.772G>A		non_coding_transcript_exon	Exon 5 of 5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD10	ENST00000267339.6	TSL:2 MANE Select	c.505G>A	p.Gly169Ser	missense	Exon 4 of 6	ENSP00000267339.2	Q9NXR5-1
	ANKRD10	ENST00000310847.8	TSL:1	c.599G>A	p.Gly200Glu	missense	Exon 5 of 5	ENSP00000312534.4	Q9NXR5-2
	ANKRD10	ENST00000465753.1	TSL:1	n.*151G>A		non_coding_transcript_exon	Exon 5 of 5	ENSP00000431927.1	Q8IUW1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.46
BayesDel_addAF	Benign	-0.059	T
BayesDel_noAF	Benign	-0.32
CADD	Pathogenic	28
DANN	Uncertain	1.0
Eigen	Pathogenic	0.89
Eigen_PC	Pathogenic	0.88
FATHMM_MKL	Uncertain	0.97	D
LIST_S2	Benign	0.47	T
M_CAP	Benign	0.081	D
MetaRNN	Uncertain	0.55	D
MetaSVM	Uncertain	-0.21	T
PhyloP100		7.2
PROVEAN	Benign	-1.0	N
REVEL	Benign	0.23
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Polyphen		1.0	D
Vest4		0.50
MutPred		0.39		Gain of loop (P = 0.0079)
MVP		0.64
ClinPred		0.99	D
GERP RS		5.9
PromoterAI		-0.0040	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.50
Mutation Taster		=12/88	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

Other links and lift over

dbSNP: rs2065130543; hg19: chr13-111545561;