5-56111514-C-T

Position:

• chr5-56111514-C-T

Variant summary

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

The NM_024669.3(ANKRD55):​c.1234G>A​(p.Asp412Asn) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 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: 6.38

Genes affected

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

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=0.16289172).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD55	NM_024669.3	c.1234G>A	p.Asp412Asn	missense_variant	10/12	ENST00000341048.9	NP_078945.2
ANKRD55	XM_047417710.1	c.748G>A	p.Asp250Asn	missense_variant	6/8		XP_047273666.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD55	ENST00000341048.9	c.1234G>A	p.Asp412Asn	missense_variant	10/12	2	NM_024669.3	ENSP00000342295	P1
ANKRD55	ENST00000434982.2	c.370G>A	p.Asp124Asn	missense_variant	2/4	1		ENSP00000429421
ANKRD55	ENST00000504958.6	c.1105G>A	p.Asp369Asn	missense_variant	8/10	5		ENSP00000424230

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 07, 2022

The c.1234G>A (p.D412N) alteration is located in exon 10 (coding exon 9) of the ANKRD55 gene. This alteration results from a G to A substitution at nucleotide position 1234, causing the aspartic acid (D) at amino acid position 412 to be replaced by an asparagine (N). 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	0.080
BayesDel_addAF	Benign	-0.18	T
BayesDel_noAF	Benign	-0.49
CADD	Benign	22
DANN	Pathogenic	1.0
DEOGEN2	Benign	0.016	T;T;.
Eigen	Benign	-0.0071
Eigen_PC	Benign	0.20
FATHMM_MKL	Uncertain	0.88	D
LIST_S2	Benign	0.80	T;T;T
M_CAP	Benign	0.0072	T
MetaRNN	Benign	0.16	T;T;T
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	0.81	L;.;.
MutationTaster	Benign	0.73	D;D;D;D
PrimateAI	Benign	0.48	T
PROVEAN	Benign	-1.3	N;N;N
REVEL	Benign	0.049
Sift	Uncertain	0.0020	D;D;D
Sift4G	Uncertain	0.0090	D;D;D
Vest4		0.13
MVP		0.40
MPC		0.28
ClinPred		0.96	D
GERP RS		5.6
Varity_R		0.16
gMVP		0.23

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: chr5-55407341;