5-56111166-C-G

Variant names:

• chr5-56111166-C-G
• NM_024669.3:c.1582G>C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_024669.3(ANKRD55):​c.1582G>C​(p.Glu528Gln) 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. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ANKRD55 NM_024669.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.49
• Publications: 0 publications found

Genes affected

ANKRD55 (HGNC:25681): (ankyrin repeat domain 55)

ENSG00000249236 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.13234153).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024669.3. 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
	ANKRD55	NM_024669.3	MANE Select	c.1582G>C	p.Glu528Gln	missense	Exon 10 of 12	NP_078945.2	Q3KP44-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD55	ENST00000341048.9	TSL:2 MANE Select	c.1582G>C	p.Glu528Gln	missense	Exon 10 of 12	ENSP00000342295.4	Q3KP44-1
	ANKRD55	ENST00000434982.2	TSL:1	c.718G>C	p.Glu240Gln	missense	Exon 2 of 4	ENSP00000429421.1	Q3KP44-2
	ANKRD55	ENST00000504958.6	TSL:5	c.1453G>C	p.Glu485Gln	missense	Exon 8 of 10	ENSP00000424230.1	D6RBD3

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	Benign	0.11
BayesDel_addAF	Benign	-0.13	T
BayesDel_noAF	Benign	-0.42
CADD	Benign	14
DANN	Uncertain	0.99
DEOGEN2	Benign	0.016	T
Eigen	Benign	0.054
Eigen_PC	Benign	0.093
FATHMM_MKL	Uncertain	0.80	D
LIST_S2	Benign	0.66	T
M_CAP	Benign	0.015	T
MetaRNN	Benign	0.13	T
MetaSVM	Benign	-0.82	T
MutationAssessor	Uncertain	2.1	M
PhyloP100		2.5
PrimateAI	Benign	0.40	T
PROVEAN	Benign	-1.2	N
REVEL	Benign	0.059
Sift	Uncertain	0.023	D
Sift4G	Uncertain	0.033	D
Vest4		0.092
MVP		0.33
MPC		0.21
ClinPred		0.74	D
GERP RS		4.7
Varity_R		0.15
gMVP		0.21
Mutation Taster		=90/10	polymorphism

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

Other links and lift over

hg19: chr5-55406993;