NM_024669.3:c.182-446G>A

Variant names:

• chr5-56176728-C-T
• rs6881896
• NM_024669.3:c.182-446G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024669.3(ANKRD55):​c.182-446G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,162 control chromosomes in the GnomAD database, including 12,158 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.30 (12158 hom., cov: 32)
• Consequence: ANKRD55 NM_024669.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490
• Publications: 2 publications found

Genes affected

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

ENSG00000296884 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD55	NM_024669.3	MANE Select	c.182-446G>A		intron	N/A	NP_078945.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD55	ENST00000341048.9	TSL:2 MANE Select	c.182-446G>A		intron	N/A	ENSP00000342295.4
	ANKRD55	ENST00000504958.6	TSL:5	c.182-446G>A		intron	N/A	ENSP00000424230.1
	ANKRD55	ENST00000513241.2	TSL:5	c.95-446G>A		intron	N/A	ENSP00000423507.2

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45309 AN: 152044 Hom.: 12115 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.238

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.298 AC: 45405 AN: 152162 Hom.: 12158 Cov.: 32 AF XY: 0.296 AC XY: 22046 AN XY: 74396

African (AFR) AF: 0.710 AC: 29484 AN: 41518

American (AMR) AF: 0.191 AC: 2918 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3470

East Asian (EAS) AF: 0.480 AC: 2483 AN: 5170

South Asian (SAS) AF: 0.196 AC: 948 AN: 4830

European-Finnish (FIN) AF: 0.119 AC: 1264 AN: 10582

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7300 AN: 67984

Other (OTH) AF: 0.238 AC: 504 AN: 2114

Alfa AF: 0.270 Hom.: 2247

Bravo AF: 0.321

Asia WGS AF: 0.358 AC: 1247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.9
DANN	Benign	0.67
PhyloP100		0.049
Mutation Taster		=100/0	polymorphism (auto)

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: rs6881896; hg19: chr5-55472555;