chr5-56111364-C-G

Position:

• chr5-56111364-C-G

Variant summary

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

The NM_024669.3(ANKRD55):​c.1384G>C​(p.Ala462Pro) 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. 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: 0.821

Genes affected

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

(HGNC:):

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=0.07397547).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD55	NM_024669.3	c.1384G>C	p.Ala462Pro	missense_variant	10/12	ENST00000341048.9
ANKRD55	XM_047417710.1	c.898G>C	p.Ala300Pro	missense_variant	6/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD55	ENST00000341048.9	c.1384G>C	p.Ala462Pro	missense_variant	10/12	2	NM_024669.3	P1
ANKRD55	ENST00000434982.2	c.520G>C	p.Ala174Pro	missense_variant	2/4	1
ANKRD55	ENST00000504958.6	c.1255G>C	p.Ala419Pro	missense_variant	8/10	5
	ENST00000645512.1			downstream_gene_variant

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 08, 2022

The c.1384G>C (p.A462P) alteration is located in exon 10 (coding exon 9) of the ANKRD55 gene. This alteration results from a G to C substitution at nucleotide position 1384, causing the alanine (A) at amino acid position 462 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.087
BayesDel_addAF	Benign	-0.20	T
BayesDel_noAF	Benign	-0.52
CADD	Benign	9.2
DANN	Benign	0.97
DEOGEN2	Benign	0.0060	T;T;.
Eigen	Benign	-0.72
Eigen_PC	Benign	-0.64
FATHMM_MKL	Benign	0.12	N
LIST_S2	Benign	0.31	T;T;T
M_CAP	Benign	0.0045	T
MetaRNN	Benign	0.074	T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.0	N;.;.
MutationTaster	Benign	1.0	N;N;N;N
PrimateAI	Benign	0.30	T
PROVEAN	Benign	-0.34	N;N;N
REVEL	Benign	0.063
Sift	Benign	0.064	T;D;T
Sift4G	Uncertain	0.019	D;D;T
Vest4		0.062
MVP		0.24
MPC		0.28
ClinPred		0.14	T
GERP RS		4.3
Varity_R		0.14
gMVP		0.20

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-55407191;