5-56116622-C-T

Position:

• chr5-56116622-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.958G>A​(p.Glu320Lys) 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. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: ANKRD55 NM_024669.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.93

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=0.23945278).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD55	NM_024669.3	c.958G>A	p.Glu320Lys	missense_variant	9/12	ENST00000341048.9	NP_078945.2
ANKRD55	XM_047417710.1	c.472G>A	p.Glu158Lys	missense_variant	5/8		XP_047273666.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD55	ENST00000341048.9	c.958G>A	p.Glu320Lys	missense_variant	9/12	2	NM_024669.3	ENSP00000342295	P1
ANKRD55	ENST00000434982.2	c.94G>A	p.Glu32Lys	missense_variant	1/4	1		ENSP00000429421
ANKRD55	ENST00000504958.6	c.829G>A	p.Glu277Lys	missense_variant	7/10	5		ENSP00000424230
ANKRD55	ENST00000505970.2	n.543G>A		non_coding_transcript_exon_variant	5/7	3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

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

Sep 01, 2021

The c.958G>A (p.E320K) alteration is located in exon 9 (coding exon 8) of the ANKRD55 gene. This alteration results from a G to A substitution at nucleotide position 958, causing the glutamic acid (E) at amino acid position 320 to be replaced by a lysine (K). 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	0.11
BayesDel_addAF	Benign	-0.034	T
BayesDel_noAF	Benign	-0.29
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.011	T;T;.
Eigen	Benign	0.083
Eigen_PC	Benign	0.16
FATHMM_MKL	Uncertain	0.89	D
LIST_S2	Uncertain	0.90	D;D;D
M_CAP	Benign	0.014	T
MetaRNN	Benign	0.24	T;T;T
MetaSVM	Benign	-0.77	T
MutationTaster	Benign	0.99	D;D;D;D
PrimateAI	Benign	0.48	T
PROVEAN	Benign	-0.91	N;N;D
REVEL	Benign	0.11
Sift	Benign	0.043	D;T;D
Sift4G	Uncertain	0.058	T;D;D
Vest4		0.45
MVP		0.72
MPC		0.67
ClinPred		0.99	D
GERP RS		3.5
Varity_R		0.18
gMVP		0.35

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: chr5-55412449;